Program options for trinity: ############################################################################### # ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.12.0 # # # Required: # # --seqType :type of reads: ('fa' or 'fq') # # --max_memory :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc) # provided in Gb of RAM, ie. '--max_memory 10G' # # If paired reads: # --left :left reads, one or more file names (separated by commas, no spaces) # --right :right reads, one or more file names (separated by commas, no spaces) # # Or, if unpaired reads: # --single :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired ) # # Or, # --samples_file tab-delimited text file indicating biological replicate relationships. # ex. # cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq # cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq # cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq # cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq # # # if single-end instead of paired-end, then leave the 4th column above empty. # #################################### ## Misc: ######################### # # --include_supertranscripts :yield supertranscripts fasta and gtf files as outputs. # # --SS_lib_type :Strand-specific RNA-Seq read orientation. # if paired: RF or FR, # if single: F or R. (dUTP method = RF) # See web documentation. # # --CPU :number of CPUs to use, default: 2 # --min_contig_length :minimum assembled contig length to report # (def=200) # # --long_reads :fasta file containing error-corrected or circular consensus (CCS) pac bio reads # (** note: experimental parameter **, this functionality continues to be under development) # # --genome_guided_bam :genome guided mode, provide path to coordinate-sorted bam file. # (see genome-guided param section under --show_full_usage_info) # # --long_reads_bam :long reads to include for genome-guided Trinity # (bam file consists of error-corrected or circular consensus (CCS) pac bio read aligned to the genome) # # --jaccard_clip :option, set if you have paired reads and # you expect high gene density with UTR # overlap (use FASTQ input file format # for reads). # (note: jaccard_clip is an expensive # operation, so avoid using it unless # necessary due to finding excessive fusion # transcripts w/o it.) # # --trimmomatic :run Trimmomatic to quality trim reads # see '--quality_trimming_params' under full usage info for tailored settings. # # --output :name of directory for output (will be # created if it doesn't already exist) # default( your current working directory: "/gscratch/scrubbed/samwhite/outputs/20230616-lsta-trinity-RNAseq/trinity_out_dir" # note: must include 'trinity' in the name as a safety precaution! ) # # --full_cleanup :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta # # --cite :show the Trinity literature citation # # --verbose :provide additional job status info during the run. # # --version :reports Trinity version (Trinity-v2.12.0) and exits. # # --show_full_usage_info :show the many many more options available for running Trinity (expert usage). # # ############################################################################### # # *Note, a typical Trinity command might be: # # Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6 # # (if you have multiple samples, use --samples_file ... see above for details) # # and for Genome-guided Trinity, provide a coordinate-sorted bam: # # Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G # --genome_guided_max_intron 10000 --CPU 6 # # see: /gscratch/srlab/programs/trinityrnaseq-v2.12.0/sample_data/test_Trinity_Assembly/ # for sample data and 'runMe.sh' for example Trinity execution # # For more details, visit: http://trinityrnaseq.github.io # ############################################################################### ---------------------------------------------- Program options for samtools_sort: samtools sort: failed to read header from "-" sort: invalid option -- 'h' Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ---------------------------------------------- Program options for samtools_view: [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". ---------------------------------------------- Program options for samtools_index: Usage: samtools index [-bc] [-m INT] [out.index] Options: -b Generate BAI-format index for BAM files [default] -c Generate CSI-format index for BAM files -m INT Set minimum interval size for CSI indices to 2^INT [14] -@ INT Sets the number of threads [none] index: invalid option -- 'h' Usage: samtools index [-bc] [-m INT] [out.index] Options: -b Generate BAI-format index for BAM files [default] -c Generate CSI-format index for BAM files -m INT Set minimum interval size for CSI indices to 2^INT [14] -@ INT Sets the number of threads [none] ---------------------------------------------- Program options for samtools_faidx: Usage: samtools faidx [ [...]] Option: -o, --output FILE Write FASTA to file. -n, --length INT Length of FASTA sequence line. [60] -c, --continue Continue after trying to retrieve missing region. -r, --region-file FILE File of regions. Format is chr:from-to. One per line. -i, --reverse-complement Reverse complement sequences. --mark-strand TYPE Add strand indicator to sequence name TYPE = rc for /rc on negative strand (default) no for no strand indicator sign for (+) / (-) custom,, for custom indicator -f, --fastq File and index in FASTQ format. -h, --help This message. ----------------------------------------------