--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: sRNA-seq Alignments - E5 Coral A.pulchra P.meandrina Using ShortStack on Mox date: '2023-06-28 14:20' tags: - sRNAseq - E5 - coral - Pocillopora meandrina - Acropora pulchra - shortstack - mox categories: - 2023 - E5 --- Steven had [asked that I align the coral E5 sRNA-seq reads using ShortStack](https://github.com/urol-e5/deep-dive/issues/19) (GitHub Issue). I previously [trimmed the sRNA-seq reads to 35bp in length](https://robertslab.github.io/sams-notebook/posts/2023/2023-06-20-Trimming-and-QC---E5-Coral-sRNA-seq-Data-fro-A.pulchra-P.evermanni-and-P.meandrina-Using--FastQC-flexbar-and-MultiQC-on-Mox/) (notebook). Next up was to actually perform the alignments using [ShortStack4](https://github.com/MikeAxtell/ShortStack). _A.pulchra_ was aligned to the _P.millepora_ genome, per [this GitHub Issue](https://github.com/urol-e5/deep-dive/issues/20#issuecomment-1574121809). This was run on Mox. NOTE: Up to this point, I've processed all three species simultaneously for which we currently have sRNA-seq data: _A.pulchra_, _P.evermanni_, and _P.meandrina_. However, [we currently haven't decided on the canonical genome to use for _P.evermanni_](https://github.com/urol-e5/deep-dive/issues/21#issuecomment-1579178682) (GitHub Issue), so _P.evermanni_ is _not_ included in this analysis. Skip to [RESULTS](#results). SLURM script (GitHub): - [20230628-E5_coral-ShortStack-sRNAseq.sh](https://github.com/RobertsLab/sams-notebook/blob/master/sbatch_scripts/20230628-E5_coral-ShortStack-sRNAseq.sh) ```bash #!/bin/bash ## Job Name #SBATCH --job-name=20230628-E5_coral-ShortStack-sRNAseq ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## Memory per node #SBATCH --mem=500G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq ### E5 sRNA-seq alignments using trimmed reads from 20230620 with ShortStack. ### Expects FastQ read directory paths to be formatted like: # /gscratch/srlab/sam/data/P_meandrina/sRNAseq/trimmed ### Uses trimmed reads from 20230620. Expect FastQ filename format like: # *flexbar_trim.20230621_[12]*.fastq.gz ################################################################################### # These variables need to be set by user ## Assign Variables # Set FastQ filename patterns fastq_pattern='**flexbar_trim.20230621*.fastq.gz' # Set number of CPUs to use threads=40 # Input/output files fastq_checksums=input_fastq_checksums.md5 sRNA_FastA="/gscratch/srlab/sam/data/miRBase/20230628-miRBase-mature.fa" # Data directories reads_dir=/gscratch/srlab/sam/data ## Inititalize arrays trimmed_fastq_array=() # Species array (must match directory name usage) species_array=("A_pulchra" "P_meandrina") # Programs associative array declare -A programs_array programs_array=( [ShortStack]="ShortStack" ) # Genomes associative array declare -A genomes_array genomes_array=( [A_pulchra]="/gscratch/srlab/sam/data/A_millepora/genomes/GCF_013753865.1_Amil_v2.1_genomic.fasta" \ [P_meandrina]="/gscratch/srlab/sam/data/P_meandrina/genomes/Pocillopora_meandrina_HIv1.assembly.fasta" ) ################################################################################### # Exit script if any command fails set -e # Load Anaconda # Uknown why this is needed, but Anaconda will not run if this line is not included. . "/gscratch/srlab/programs/anaconda3/etc/profile.d/conda.sh" # Activate flexbar environment conda activate ShortStack4_env # Set working directory working_dir=$(pwd) for species in "${species_array[@]}" do ## Inititalize arrays trimmed_fastq_array=() echo "Creating ${species} directory ..." mkdir --parents "${species}" # Change to species directory cd "${species}" # ShortStack output directory output_dir=$(pwd) echo "Now in ${PWD}." # Sync raw FastQ files to working directory echo "" echo "Transferring files via rsync..." rsync --archive --verbose \ ${reads_dir}/${species}/sRNAseq/trimmed/${fastq_pattern} . echo "" echo "File transfer complete." echo "" ### Run ShortStack ### ### NOTE: Do NOT quote trimmed_fastq_list # Create array of trimmed FastQs trimmed_fastq_array=(${fastq_pattern}) # Pass array contents to new variable as space-delimited list trimmed_fastq_list=$(echo "${trimmed_fastq_array[*]}") echo "Beginning ShortStack on ${species} sRNAseq using genome FastA:" echo "${genomes_array[${species}]}" echo "" ## Run ShortStack ## ${programs_array[ShortStack]} \ --genomefile "${genomes_array[${species}]}" \ --readfile ${trimmed_fastq_list} \ --known_miRNAs ${sRNA_FastA} \ --dn_mirna \ --threads ${threads} \ --outdir ${output_dir}/ShortStack_out echo "ShortStack on ${species} complete!" echo "" ######## Create MD5 checksums for raw FastQs ######## for fastq in ${fastq_pattern} do echo "Generating checksum for ${fastq}" md5sum "${fastq}" | tee --append ${fastq_checksums} echo "" done ######## END MD5 CHECKSUMS ######## ######## REMOVE INPUT FASTQS ######## echo "Removing input FastQs." echo "" rm ${fastq_pattern} echo "Input FastQs removed." echo"" echo "Now moving back to ${working_dir}." cd "${working_dir}" echo "" done #################################################################### # Capture program options if [[ "${#programs_array[@]}" -gt 0 ]]; then echo "Logging program options..." for program in "${!programs_array[@]}" do { echo "Program options for ${program}: " echo "" # Handle samtools help menus if [[ "${program}" == "samtools_index" ]] \ || [[ "${program}" == "samtools_sort" ]] \ || [[ "${program}" == "samtools_view" ]] then ${programs_array[$program]} # Handle DIAMOND BLAST menu elif [[ "${program}" == "diamond" ]]; then ${programs_array[$program]} help # Handle NCBI BLASTx menu elif [[ "${program}" == "blastx" ]]; then ${programs_array[$program]} -help # Handle fastp menu elif [[ "${program}" == "fastp" ]]; then ${programs_array[$program]} --help else ${programs_array[$program]} -h fi echo "" echo "" echo "----------------------------------------------" echo "" echo "" } &>> program_options.log || true # If MultiQC is in programs_array, copy the config file to this directory. if [[ "${program}" == "multiqc" ]]; then cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml fi done fi # Document programs in PATH (primarily for program version ID) { date echo "" echo "System PATH for $SLURM_JOB_ID" echo "" printf "%0.s-" {1..10} echo "${PATH}" | tr : \\n } >> system_path.log ``` --- # RESULTS Run time seemed relatively fast; just a bit over 4hrs: ![Screencap showing ShortStack runtime on Mox of 4hrs 11mins 59secs](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20230628-E5_coral-ShortStack-sRNAseq-runtime.png?raw=true) The results and links to various files are below. At this time, I have not done any evaluation of the results, nor have I looked into the [ShortStack](https://github.com/MikeAxtell/ShortStack) documentation to read how the results are formatted; will leave this for a future date and/or somebody else. Output folder: - [20230628-E5_coral-ShortStack-sRNAseq/](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/) ### [_A.pulchra_](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/) - #### Results files: - [alignment_details.tsv](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/alignment_details.tsv) (48K) - MD5: `d301b898b36c2022f22db538fa28b9eb` | readfile | mapping_type | read_length | count | |---------------------------------------------------------------------------------------------------------------------------------------------------|--------------|-------------|---------| | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | <21 | 120030 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | 21 | 43333 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | 22 | 105592 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | 23 | 65039 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | 24 | 84409 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | U | >24 | 3636233 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | <21 | 196501 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | 21 | 61672 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | 22 | 73193 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | 23 | 69147 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | 24 | 73631 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | P | >24 | 5674586 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | <21 | 25655 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | 21 | 11222 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | 22 | 12916 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | 23 | 14482 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | 24 | 19433 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | R | >24 | 1400108 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | <21 | 7685 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | 21 | 2697 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | 22 | 3260 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | 23 | 3166 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | 24 | 4394 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | H | >24 | 238409 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | <21 | 104184 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | 21 | 60191 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | 22 | 52988 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | 23 | 59083 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | 24 | 76366 | | /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam | N | >24 | 5252357 | - [Counts.txt](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/Counts.txt) (1.3M) - MD5: `593069a45787e4176c5e17efe3b87d49` | Coords | Name | MIRNA | sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1 | sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2 | sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1 | sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2 | sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1 | sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_2 | sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_1 | sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_2 | sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_1 | sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_2 | |---------------------------|-----------|-------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------|---------------------------------------------| | NC_058066.1:152483-152906 | Cluster_1 | N | 1 | 3 | 126 | 137 | 1 | 2 | 2 | 2 | 2 | 3 | | NC_058066.1:161082-161790 | Cluster_2 | N | 46 | 57 | 48 | 54 | 210 | 319 | 33 | 25 | 190 | 270 | | NC_058066.1:203244-203650 | Cluster_3 | N | 17 | 15 | 37 | 30 | 11 | 15 | 15 | 10 | 41 | 33 | | NC_058066.1:204535-205150 | Cluster_4 | N | 6 | 6 | 270 | 254 | 18 | 16 | 12 | 6 | 56 | 59 | | NC_058066.1:205746-206966 | Cluster_5 | N | 82 | 93 | 450 | 453 | 66 | 71 | 253 | 239 | 239 | 127 | | NC_058066.1:210855-211344 | Cluster_6 | N | 340 | 351 | 213 | 210 | 83 | 81 | 0 | 1 | 656 | 647 | | NC_058066.1:349656-351297 | Cluster_7 | N | 497 | 510 | 1246 | 1247 | 841 | 772 | 768 | 762 | 19 | 21 | | NC_058066.1:351491-353439 | Cluster_8 | N | 3253 | 3186 | 2069 | 2014 | 2158 | 2159 | 2113 | 2084 | 169 | 174 | | NC_058066.1:776275-776779 | Cluster_9 | N | 0 | 0 | 318 | 280 | 10 | 11 | 58 | 61 | 180 | 175 | - [Results.txt](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/Results.txt) (2.8M) - MD5: `0ae9d3267579e8614e57a73a3490430d` | Locus | Name | Chrom | Start | End | Length | Reads | UniqueReads | FracTop | Strand | MajorRNA | MajorRNAReads | Short | Long | 21 | 22 | 23 | 24 | DicerCall | MIRNA | known_miRNAs | |---------------------------|-----------|-------------|--------|--------|--------|-------|-------------|-------------------|--------|--------------------------------|---------------|-------|-------|----|-----|-----|-----|-----------|-------|--------------| | NC_058066.1:152483-152906 | Cluster_1 | NC_058066.1 | 152483 | 152906 | 424 | 279 | 77 | 0.512544802867383 | . | UAAGUACUUUAUCAACUAACUCUAGGCA | 77 | 3 | 260 | 0 | 3 | 0 | 13 | N | N | NA | | NC_058066.1:161082-161790 | Cluster_2 | NC_058066.1 | 161082 | 161790 | 709 | 1252 | 475 | 0.623801916932907 | . | AGUCGACGAAUUUGCCAUGAAGCUAGUA | 71 | 39 | 1129 | 26 | 10 | 5 | 43 | N | N | NA | | NC_058066.1:203244-203650 | Cluster_3 | NC_058066.1 | 203244 | 203650 | 407 | 224 | 112 | 0.535714285714286 | . | UUCUGACUCUAUUAGCAACGAAGACUUU | 38 | 2 | 217 | 2 | 1 | 0 | 2 | N | N | NA | | NC_058066.1:204535-205150 | Cluster_4 | NC_058066.1 | 204535 | 205150 | 616 | 703 | 343 | 0.500711237553343 | . | UCCCAACACGUCUAGACUGUACAAUUUCU | 33 | 4 | 682 | 2 | 0 | 7 | 8 | N | N | NA | | NC_058066.1:205746-206966 | Cluster_5 | NC_058066.1 | 205746 | 206966 | 1221 | 2073 | 732 | 0.535455861070912 | . | CAAAAGAGCGGACAAAAUAGUCGACAGAUU | 152 | 15 | 1999 | 8 | 6 | 13 | 32 | N | N | NA | | NC_058066.1:210855-211344 | Cluster_6 | NC_058066.1 | 210855 | 211344 | 490 | 2582 | 667 | 0.497676219984508 | . | UAAUACUUGUAGUGAAGGUUCAAUCUCGA | 97 | 17 | 2355 | 13 | 18 | 39 | 140 | N | N | NA | | NC_058066.1:349656-351297 | Cluster_7 | NC_058066.1 | 349656 | 351297 | 1642 | 6683 | 2375 | 0.501571150680832 | . | UCAGCUUGGAAAUGACAGCUUUUGACGU | 294 | 53 | 6417 | 22 | 45 | 44 | 102 | N | N | NA | | NC_058066.1:351491-353439 | Cluster_8 | NC_058066.1 | 351491 | 353439 | 1949 | 19379 | 3490 | 0.498632540378761 | . | UUUCAAAUCAAAGAUCUUCGCAACGAUGA | 1115 | 135 | 18526 | 59 | 101 | 247 | 311 | N | N | NA | | NC_058066.1:776275-776779 | Cluster_9 | NC_058066.1 | 776275 | 776779 | 505 | 1093 | 284 | 0.517840805123513 | . | UGUUAUUGUCUUUGAGUGCCCAAAUGUGU | 64 | 3 | 1080 | 2 | 3 | 2 | 3 | N | N | NA | - #### GFFs: - [Results.gff3](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/Results.gff3) (1.8M) - MD5: `84be69fd3fc4a02fd64c83ad0cbdaa63` - [known_miRNAs.gff3](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.gff3) (88K) - MD5: `d9c407fde49dad766805eed720ef56b0` - #### BAMs: - [merged_alignments.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/merged_alignments.bam) (3.2G) - MD5: `6cdc0a903f5761528518453c5cf735c4` - [sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam) (301M) - MD5: `519cb501a0f5fa32539d3571c9017929` - [sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2.bam) (307M) - MD5: `4b01b68a60ae5563c1dbada3eae9cde9` - [sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1.bam) (337M) - MD5: `3347abd91870d380d719281e091571a0` - [sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2.bam) (340M) - MD5: `056895a4d142c5c0bc0cd0ea52f866a7` - [sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1.bam) (358M) - MD5: `968fcf9472f4d9da500878a7bc4d4e87` ### [_P.meandrina_](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/) - #### Results files: - [Counts.txt](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/Counts.txt) (684K) - MD5: `45c7fa265a74c685ce60848447fa4566` | Coords | Name | MIRNA | sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1 | sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2 | sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1 | sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2 | sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1 | sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2 | sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1 | sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2 | sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1 | sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2 | |------------------------------------------------------|-----------|-------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------|--------------------------------------------| | Pocillopora_meandrina_HIv1___Sc0000000:9091-9526 | Cluster_1 | N | 1828 | 1784 | 1393 | 1412 | 1842 | 1812 | 3219 | 3286 | 3565 | 3477 | | Pocillopora_meandrina_HIv1___Sc0000000:53578-53997 | Cluster_2 | N | 24 | 24 | 52 | 53 | 67 | 67 | 53 | 55 | 95 | 91 | | Pocillopora_meandrina_HIv1___Sc0000000:146768-147202 | Cluster_3 | N | 3 | 248 | 2 | 73 | 0 | 116 | 0 | 107 | 5 | 226 | | Pocillopora_meandrina_HIv1___Sc0000000:150243-150718 | Cluster_4 | N | 437 | 422 | 691 | 676 | 813 | 804 | 692 | 700 | 1021 | 1007 | | Pocillopora_meandrina_HIv1___Sc0000000:173728-174150 | Cluster_5 | N | 171 | 167 | 169 | 167 | 269 | 271 | 317 | 318 | 336 | 334 | | Pocillopora_meandrina_HIv1___Sc0000000:187648-188072 | Cluster_6 | N | 8 | 7 | 16 | 13 | 28 | 27 | 59 | 72 | 76 | 76 | | Pocillopora_meandrina_HIv1___Sc0000000:485727-486254 | Cluster_7 | N | 114 | 112 | 98 | 96 | 49 | 50 | 165 | 168 | 270 | 259 | | Pocillopora_meandrina_HIv1___Sc0000000:525310-527341 | Cluster_8 | N | 3753 | 3707 | 1260 | 1254 | 4711 | 4627 | 2811 | 2878 | 2607 | 2572 | | Pocillopora_meandrina_HIv1___Sc0000000:541262-541723 | Cluster_9 | N | 127 | 130 | 86 | 91 | 85 | 96 | 331 | 317 | 85 | 87 | - [Results.txt](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/Results.txt) (1.4M) - MD5: `7b96db202d049a53f154ee3fc1fcda08` ``` Locus Name Chrom Start End Length Reads UniqueReads FracTop Strand MajorRNA MajorRNAReads Short Long 21 22 23 24 DicerCall MIRNA known_miRNAs Pocillopora_meandrina_HIv1___Sc0000000:9091-9526 Cluster_1 Pocillopora_meandrina_HIv1___Sc0000000 9091 9526 436 23618 903 0.501566601744432 . UCUACCACUGAGCUAUACCCCC 3810 2853 9677 1223 8614 359 892 N N NA Pocillopora_meandrina_HIv1___Sc0000000:53578-53997 Cluster_2 Pocillopora_meandrina_HIv1___Sc0000000 53578 53997 420 581 27 0.500860585197935 . GCCUAAGUUGCUUGGAACA 142 577 4 0 0 0 0 N N NA Pocillopora_meandrina_HIv1___Sc0000000:146768-147202 Cluster_3 Pocillopora_meandrina_HIv1___Sc0000000 146768 147202 435 780 108 0.971794871794872 + AGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 267 2 773 4 0 1 0 N N NA Pocillopora_meandrina_HIv1___Sc0000000:150243-150718 Cluster_4 Pocillopora_meandrina_HIv1___Sc0000000 150243 150718 476 7263 645 0.496902106567534 . UUAUGUGAUGAGUAUGUUAAUGUACUCUCUGAGC 566 1692 2932 1272 749 280 338 N N NA Pocillopora_meandrina_HIv1___Sc0000000:173728-174150 Cluster_5 Pocillopora_meandrina_HIv1___Sc0000000 173728 174150 423 2519 134 0.500992457324335 . CAACCAGAUCACAGCAAUCAAA 438 212 8 83 1269 887 60 22 N NA Pocillopora_meandrina_HIv1___Sc0000000:187648-188072 Cluster_6 Pocillopora_meandrina_HIv1___Sc0000000 187648 188072 425 382 74 0.523560209424084 . AUAAAUGUCACUACAAGAAACCUGAAAUCGU 25 1 366 2 2 4 7 N N NA Pocillopora_meandrina_HIv1___Sc0000000:485727-486254 Cluster_7 Pocillopora_meandrina_HIv1___Sc0000000 485727 486254 528 1381 391 0.503982621288921 . UUGCACUAGAACAGACUGUGCUUCCAUAUCAGCUG 152 132 1174 14 22 6 33 N N NA Pocillopora_meandrina_HIv1___Sc0000000:525310-527341 Cluster_8 Pocillopora_meandrina_HIv1___Sc0000000 525310 527341 2032 30180 6208 0.498939695162359 . UUUUCGUCACUUUCUUCAGCCUCAGAGU 973 277 27960 102 211 625 1005 N N NA Pocillopora_meandrina_HIv1___Sc0000000:541262-541723 Cluster_9 Pocillopora_meandrina_HIv1___Sc0000000 541262 541723 462 1435 283 0.500348432055749 . UUGGACGAAAUUUCGAGGUUCACACUCGUU 86 0 1425 0 7 2 1 N N NA ``` - [alignment_details.tsv](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/alignment_details.tsv) (48K) - MD5: `b89a4d5f7d1c49fcc8b3c31fdb316837` ``` readfile mapping_type read_length count /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U <21 277334 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U 21 114752 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U 22 331234 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U 23 133358 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U 24 46856 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam U >24 1441069 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P <21 472110 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P 21 109577 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P 22 119506 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P 23 96527 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P 24 73770 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam P >24 3922569 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R <21 270975 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R 21 95814 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R 22 130073 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R 23 82638 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R 24 190938 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam R >24 1254706 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H <21 20811 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H 21 5811 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H 22 5117 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H 23 5552 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H 24 5909 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam H >24 47393 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N <21 122944 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N 21 59503 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N 22 101407 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N 23 92953 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N 24 117111 /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam N >24 5315658 ``` - #### GFFs: - [Results.gff3](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/Results.gff3) (860K) - MD5: `6dde17bf837ca3ee56534fb638a655cf` - [known_miRNAs.gff3](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.gff3) (160K) - #### BAMs: - [merged_alignments.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/merged_alignments.bam) (2.5G) - MD5: `a8fe8903ee2690b925768c205ef88692` - [sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam) (227M) - MD5: `0d411052dc3a4b0ffe05dbe2dc695e27` - [sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2.bam) (232M) - MD5: `b9450ad15e29061565516d079a77e111` - [sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1.bam) (236M) - MD5: `09c05641624ce2f26cec91df6ab2e51d` - [sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2.bam) (240M) - MD5: `a0c4cf038cc37be46c863c2be831b00c` - [sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1.bam) (220M) - MD5: `347284e0c5b0fa8f049a26a075f8b82a` - [sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2.bam) (222M) - MD5: `2c3fb0d9d557c572f4bd10541d56f603` - [sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1.bam) (282M) - MD5: `cd31c3f587e4e6aa13acb00fd2fe67a3` - [sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2.bam) (278M) - MD5: `f09c6a03df26536d90c7f80262911d3a` - [sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1.bam) (255M) - MD5: `b55a29681e8979e09486c2abc16c492f` - [sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2.bam](https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2.bam) (259M) - MD5: `26e92bb5edec78b2d613065a52272ea0`