This notebook performs a simple NCBI BLASTn [@altschul1990] against two miRNA databases to attempt to identify miRNA in P.evermanni sRNAseq:
Relies on the following software:
fastx_collapser: Collapses duplicate sequences in FastA/Q into single sequence.This allows usage of Bash variables across R Markdown chunks.
{
echo "#### Assign Variables ####"
echo ""
echo "# Trimmed FastQ naming pattern"
echo "export trimmed_fastqs_pattern='*-31bp-merged.fq.gz'"
echo "# Data directories"
echo 'export deep_dive_dir=/home/shared/8TB_HDD_02/shedurkin/deep-dive'
echo 'export deep_dive_data_dir="${deep_dive_dir}/data"'
echo 'export output_dir_top=${deep_dive_dir}/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged'
echo 'export trimmed_fastqs_dir="${deep_dive_dir}/E-Peve/output/06.2-Peve-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads"'
echo 'export blast_dbs_dir="${deep_dive_dir}/data/blast_dbs"'
echo ""
echo "# Input/Output files"
echo 'export collapsed_reads_fasta="collapsed-reads-all.fasta"'
echo 'export concatenated_trimmed_reads_fastq="concatenated-trimmed-reads-all.fastq.gz"'
echo 'export mirbase_mature_fasta_name="mirbase-mature-v22.1.fa"'
echo 'export mirbase_mature_fasta_no_U="mirbase-mature-v22.1-no_U.fa"'
echo 'export mirgene_mature_fasta_name="mirgene-mature-all-v2.1.fa"'
echo 'export mirgene_mature_fasta_no_U="mirgene-mature-all-v2.1-no_U.fa"'
echo ""
echo "# External data URLs"
echo 'export mirgenedb_fasta_url="https://www.mirgenedb.org/fasta/ALL?mat=1"'
echo ""
echo "# Paths to programs"
echo 'export ncbi_blast_dir="/home/shared/ncbi-blast-2.15.0+/bin/"'
echo 'export ncbi_blastn="${ncbi_blast_dir}/blastn"'
echo 'export ncbi_makeblast_db="${ncbi_blast_dir}/makeblastdb"'
echo 'export fastx_collapser="/home/shared/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64/bin/fastx_collapser"'
echo "# Set number of CPUs to use"
echo 'export threads=46'
echo ""
echo "# Initialize arrays"
echo 'export trimmed_fastqs_array=()'
} > .bashvars
cat .bashvars#### Assign Variables ####
# Trimmed FastQ naming pattern
export trimmed_fastqs_pattern='*-31bp-merged.fq.gz'
# Data directories
export deep_dive_dir=/home/shared/8TB_HDD_02/shedurkin/deep-dive
export deep_dive_data_dir="${deep_dive_dir}/data"
export output_dir_top=${deep_dive_dir}/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged
export trimmed_fastqs_dir="${deep_dive_dir}/E-Peve/output/06.2-Peve-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads"
export blast_dbs_dir="${deep_dive_dir}/data/blast_dbs"
# Input/Output files
export collapsed_reads_fasta="collapsed-reads-all.fasta"
export concatenated_trimmed_reads_fastq="concatenated-trimmed-reads-all.fastq.gz"
export mirbase_mature_fasta_name="mirbase-mature-v22.1.fa"
export mirbase_mature_fasta_no_U="mirbase-mature-v22.1-no_U.fa"
export mirgene_mature_fasta_name="mirgene-mature-all-v2.1.fa"
export mirgene_mature_fasta_no_U="mirgene-mature-all-v2.1-no_U.fa"
# External data URLs
export mirgenedb_fasta_url="https://www.mirgenedb.org/fasta/ALL?mat=1"
# Paths to programs
export ncbi_blast_dir="/home/shared/ncbi-blast-2.15.0+/bin/"
export ncbi_blastn="${ncbi_blast_dir}/blastn"
export ncbi_makeblast_db="${ncbi_blast_dir}/makeblastdb"
export fastx_collapser="/home/shared/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64/bin/fastx_collapser"
# Set number of CPUs to use
export threads=46
# Initialize arrays
export trimmed_fastqs_array=()# Load bash variables into memory
source .bashvars
wget \
--no-check-certificate \
--continue \
--no-host-directories \
--no-directories \
--no-parent \
--quiet \
--execute robots=off \
--output-document ${deep_dive_data_dir}/${mirgene_mature_fasta_name} \
${mirgenedb_fasta_url}
ls -lh ${deep_dive_data_dir}total 17M
drwxr-xr-x 2 shedurkin labmembers 4.0K Nov 14 09:39 blast_dbs
-rw-r--r-- 1 shedurkin labmembers 3.8M Apr 11 10:12 cnidarian-mirbase-mature-v22.1.fasta
-rw-r--r-- 1 shedurkin labmembers 44K Apr 11 10:12 cnidarian_miRNAs.fasta
-rw-r--r-- 1 shedurkin labmembers 3.7M Apr 11 10:38 mirbase-mature-v22.1.fa
-rw-r--r-- 1 shedurkin labmembers 3.7M Dec 5 11:39 mirbase-mature-v22.1-no_spaces.fa
-rw-r--r-- 1 shedurkin labmembers 3.7M Apr 15 09:11 mirbase-mature-v22.1-no_U.fa
-rw-r--r-- 1 shedurkin labmembers 726K Nov 14 09:39 mirgene-mature-all-v2.1.fa
-rw-r--r-- 1 shedurkin labmembers 726K Apr 15 09:11 mirgene-mature-all-v2.1-no_U.fa# Load bash variables into memory
source .bashvars
head "${deep_dive_data_dir}"/mir*.fa==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1.fa <==
>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CAUACUUCCUUACAUGCCCAUA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa <==
>cel-let-7-5p_MIMAT0000001_Caenorhabditis_elegans_let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p_MIMAT0015091_Caenorhabditis_elegans_let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p_MIMAT0000002_Caenorhabditis_elegans_lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p_MIMAT0015092_Caenorhabditis_elegans_lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p_MIMAT0020301_Caenorhabditis_elegans_miR-1-5p
CAUACUUCCUUACAUGCCCAUA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_U.fa <==
>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
TGAGGTAGTAGGTTGTATAGTT
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CTATGCAATTTTCTACCTTACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
TCCCTGAGACCTCAAGTGTGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCTGGGCTCTCCGGGTACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CATACTTCCTTACATGCCCATA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirgene-mature-all-v2.1.fa <==
>Aae-Bantam_3p
UGAGAUCAUUUUGAAAGCUGAUU
>Bge-Bantam_3p
UGAGAUCAUUGUGAAAGCUGAUU
>Bpl-Bantam_3p
UGAGAUCAUUGUGAAAACUGAU
>Cgi-Bantam_3p
UGAGAUCAUUGUGAAAACUGAUU
>Cte-Bantam_3p
UGAGAUCAUUGUGAAAACUAAUC
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirgene-mature-all-v2.1-no_U.fa <==
>Aae-Bantam_3p
TGAGATCATTTTGAAAGCTGATT
>Bge-Bantam_3p
TGAGATCATTGTGAAAGCTGATT
>Bpl-Bantam_3p
TGAGATCATTGTGAAAACTGAT
>Cgi-Bantam_3p
TGAGATCATTGTGAAAACTGATT
>Cte-Bantam_3p
TGAGATCATTGTGAAAACTAATCU to T in miRNA FastAsThis is needed because the sRNAseq sequences do not have uracils (U) - they have thymines (T).
# Load bash variables into memory
source .bashvars
# Convert miRBase FastA
sed '/^[^>]/s/U/T/g' "${deep_dive_data_dir}/${mirbase_mature_fasta_name}" \
> "${deep_dive_data_dir}/${mirbase_mature_fasta_no_U}"
# Convert MirGene FastA
sed '/^[^>]/s/U/T/g' "${deep_dive_data_dir}/${mirgene_mature_fasta_name}" \
> "${deep_dive_data_dir}/${mirgene_mature_fasta_no_U}"
head ${deep_dive_data_dir}/*.fa
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1.fa <==
>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CAUACUUCCUUACAUGCCCAUA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa <==
>cel-let-7-5p_MIMAT0000001_Caenorhabditis_elegans_let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p_MIMAT0015091_Caenorhabditis_elegans_let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p_MIMAT0000002_Caenorhabditis_elegans_lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p_MIMAT0015092_Caenorhabditis_elegans_lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p_MIMAT0020301_Caenorhabditis_elegans_miR-1-5p
CAUACUUCCUUACAUGCCCAUA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_U.fa <==
>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
TGAGGTAGTAGGTTGTATAGTT
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CTATGCAATTTTCTACCTTACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
TCCCTGAGACCTCAAGTGTGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCTGGGCTCTCCGGGTACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CATACTTCCTTACATGCCCATA
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirgene-mature-all-v2.1.fa <==
>Aae-Bantam_3p
UGAGAUCAUUUUGAAAGCUGAUU
>Bge-Bantam_3p
UGAGAUCAUUGUGAAAGCUGAUU
>Bpl-Bantam_3p
UGAGAUCAUUGUGAAAACUGAU
>Cgi-Bantam_3p
UGAGAUCAUUGUGAAAACUGAUU
>Cte-Bantam_3p
UGAGAUCAUUGUGAAAACUAAUC
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirgene-mature-all-v2.1-no_U.fa <==
>Aae-Bantam_3p
TGAGATCATTTTGAAAGCTGATT
>Bge-Bantam_3p
TGAGATCATTGTGAAAGCTGATT
>Bpl-Bantam_3p
TGAGATCATTGTGAAAACTGAT
>Cgi-Bantam_3p
TGAGATCATTGTGAAAACTGATT
>Cte-Bantam_3p
TGAGATCATTGTGAAAACTAATC# Load bash variables into memory
source .bashvars
# miRBase BLAST DB
## Make sure output directory exists
if [ ! -d "${blast_dbs_dir}" ]; then
mkdir --parents "${blast_dbs_dir}"
fi
## Check for pre-exising database
if [ ! -f "${blast_dbs_dir}/${mirgene_mature_fasta_no_U%.*}.blastdb.log" ]; then
${ncbi_makeblast_db} \
-in ${deep_dive_data_dir}/${mirgene_mature_fasta_no_U} \
-title ${mirgene_mature_fasta_no_U%.*} \
-dbtype nucl \
-out ${blast_dbs_dir}/${mirgene_mature_fasta_no_U%.*} \
-logfile ${blast_dbs_dir}/${mirgene_mature_fasta_no_U%.*}.blastdb.log
fi
# miRBase BLAST DB
## Make sure output directory exists
if [ ! -d "${blast_dbs_dir}" ]; then
mkdir --parents "${blast_dbs_dir}"
fi
## Check for pre-exising database
if [ ! -f "${blast_dbs_dir}/${mirbase_mature_fasta_no_U%.*}.blastdb.log" ]; then
${ncbi_makeblast_db} \
-in ${deep_dive_data_dir}/${mirbase_mature_fasta_no_U} \
-title ${mirbase_mature_fasta_no_U%.*} \
-dbtype nucl \
-out ${blast_dbs_dir}/${mirbase_mature_fasta_no_U%.*} \
-logfile ${blast_dbs_dir}/${mirbase_mature_fasta_no_U%.*}.blastdb.log
fi# Load bash variables into memory
source .bashvars
# Check for existence of concatenated FastA before running
if [ ! -f "${output_dir_top}/${concatenated_trimmed_reads_fastq}" ]; then
cat ${trimmed_fastqs_dir}/*.gz \
> "${output_dir_top}/${concatenated_trimmed_reads_fastq}"
fi
ls -lh "${output_dir_top}/${concatenated_trimmed_reads_fastq}"-rw-r--r-- 1 shedurkin labmembers 694M Apr 12 09:35 /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/concatenated-trimmed-reads-all.fastq.gzUses fastx_collapser to collapse to unique reads.
Requires undocumented quality setting. Have selected 30 as cuttoff: -Q30.
# Load bash variables into memory
source .bashvars
# Check for existence of collapsed FastA before running
time \
if [ ! -f "${output_dir_top}/${collapsed_reads_fasta}" ]; then
zcat ${output_dir_top}/${concatenated_trimmed_reads_fastq} \
| ${fastx_collapser} \
-Q30 \
-o "${output_dir_top}/${collapsed_reads_fasta}"
fi
head "${output_dir_top}/${collapsed_reads_fasta}"
echo ""
echo ""
total_reads=$(grep -c "^>" ${output_dir_top}/${collapsed_reads_fasta})
echo "Total number of reads after collapse: ${total_reads}"
real 0m0.000s
user 0m0.000s
sys 0m0.000s
>1-2039267
TGAAAATCTTTGCTCTGAAGTGGAA
>2-1218024
GCACTGGTGGTTCAGTGGTAGAATTCTCGCC
>3-551889
GCACTGGTGGTTCAGTGGTAGAATTCTCGCT
>4-472935
GTGTGCTTAAGCGTGAGTAGTTGTCT
>5-375248
GTGTGCTTAAGCGTGAGTAGTTGTCTGCT
Total number of reads after collapse: 4555070Runs BLASTn using the blastn-short task for sequences < 30bp.
Look for top match (-max_hsps 1 & -max_target_seqs 1) for each query.
Examining 5 or more matches is recommended by
redirecting stdout: 2> /dev/null# Load bash variables into memory
source .bashvars
time \
${ncbi_blastn} \
-db ${blast_dbs_dir}/${mirbase_mature_fasta_no_U%.*} \
-query ${output_dir_top}/${collapsed_reads_fasta} \
-out ${output_dir_top}/miRBase-BLASTn-eval_1000.outfmt6 \
-task blastn-short \
-max_hsps 1 \
-max_target_seqs 1 \
-outfmt 6 \
-num_threads ${threads} \
2> /dev/null# Load bash variables into memory
source .bashvars
time \
${ncbi_blastn} \
-db ${blast_dbs_dir}/${mirgene_mature_fasta_no_U%.*} \
-query ${output_dir_top}/${collapsed_reads_fasta} \
-out ${output_dir_top}/MirGene-BLASTn-eval_1000.outfmt6 \
-task blastn-short \
-max_hsps 1 \
-max_target_seqs 1 \
-outfmt 6 \
-num_threads ${threads} \
2> /dev/nullRunning this for simple comparison to the default blastn-short value of 1000.
# Load bash variables into memory
source .bashvars
time \
${ncbi_blastn} \
-db ${blast_dbs_dir}/${mirbase_mature_fasta_no_U%.*} \
-query ${output_dir_top}/${collapsed_reads_fasta} \
-out ${output_dir_top}/miRBase-BLASTn-eval_10.outfmt6 \
-task blastn-short \
-evalue 10 \
-max_hsps 1 \
-max_target_seqs 1 \
-outfmt 6 \
-num_threads ${threads} \
2> /dev/null# Load bash variables into memory
source .bashvars
time \
${ncbi_blastn} \
-db ${blast_dbs_dir}/${mirgene_mature_fasta_no_U%.*} \
-query ${output_dir_top}/${collapsed_reads_fasta} \
-out ${output_dir_top}/MirGene-BLASTn-eval_10.outfmt6 \
-task blastn-short \
-evalue 10 \
-max_hsps 1 \
-max_target_seqs 1 \
-outfmt 6 \
-num_threads ${threads} \
2> /dev/null# Load bash variables into memory
source .bashvars
head ${output_dir_top}/*eval_1000.outfmt6
echo ""
echo "-----------------------------------------"
echo ""
wc -l ${output_dir_top}/*eval_1000.outfmt6==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/miRBase-BLASTn-eval_1000.outfmt6 <==
1-2039267 ssc-miR-7143-5p 100.000 11 0 0 12 22 8 18 1.4 22.3
2-1218024 ppc-miR-8214-5p 100.000 13 0 0 12 24 18 6 0.11 26.3
3-551889 ppc-miR-8214-5p 100.000 13 0 0 12 24 18 6 0.11 26.3
4-472935 lja-miR11150-3p 100.000 10 0 0 13 22 10 19 6.1 20.3
5-375248 rlcv-miR-rL1-23-3p 100.000 11 0 0 18 28 2 12 1.8 22.3
6-292862 cpo-miR-1379-5p 100.000 12 0 0 1 12 18 7 0.29 24.3
7-292012 cpo-miR-1379-5p 100.000 12 0 0 1 12 18 7 0.34 24.3
8-258161 mdo-miR-12324a-3p 100.000 11 0 0 3 13 11 1 2.0 22.3
9-226514 cpo-miR-1379-5p 100.000 12 0 0 2 13 18 7 0.36 24.3
10-214759 oni-miR-10971 100.000 11 0 0 16 26 8 18 1.8 22.3
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/MirGene-BLASTn-eval_1000.outfmt6 <==
1-2039267 Tca-Mir-87-P2_3p 100.000 11 0 0 5 15 13 3 0.54 22.3
2-1218024 Pma-Mir-96-P3o2_5p 100.000 11 0 0 16 26 9 19 0.78 22.3
3-551889 Pma-Mir-96-P3o2_5p 100.000 11 0 0 16 26 9 19 0.78 22.3
4-472935 Dno-Mir-1271_5p 100.000 9 0 0 1 9 21 13 9.1 18.3
5-375248 Bla-Mir-4857_5p 100.000 9 0 0 21 29 10 18 11 18.3
6-292862 Mml-Mir-2114_5p 100.000 10 0 0 13 22 11 20 2.0 20.3
7-292012 Mml-Mir-2114_5p 100.000 10 0 0 13 22 11 20 2.0 20.3
8-258161 Mdo-Mir-7398-P25_3p 100.000 10 0 0 15 24 10 1 2.9 20.3
9-226514 Mml-Mir-2114_5p 100.000 10 0 0 14 23 11 20 2.2 20.3
10-214759 Cin-Mir-4053_3p 100.000 9 0 0 5 13 14 22 12 18.3
-----------------------------------------
4555070 /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/miRBase-BLASTn-eval_1000.outfmt6
4555070 /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/MirGene-BLASTn-eval_1000.outfmt6
9110140 total# Load bash variables into memory
source .bashvars
head ${output_dir_top}/*eval_10.outfmt6
echo ""
echo "-----------------------------------------"
echo ""
wc -l ${output_dir_top}/*eval_10.outfmt6==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/miRBase-BLASTn-eval_10.outfmt6 <==
1-2039267 ssc-miR-7143-5p 100.000 11 0 0 12 22 8 18 1.4 22.3
2-1218024 ppc-miR-8214-5p 100.000 13 0 0 12 24 18 6 0.11 26.3
3-551889 ppc-miR-8214-5p 100.000 13 0 0 12 24 18 6 0.11 26.3
4-472935 lja-miR11150-3p 100.000 10 0 0 13 22 10 19 6.1 20.3
5-375248 rlcv-miR-rL1-23-3p 100.000 11 0 0 18 28 2 12 1.8 22.3
6-292862 cpo-miR-1379-5p 100.000 12 0 0 1 12 18 7 0.29 24.3
7-292012 cpo-miR-1379-5p 100.000 12 0 0 1 12 18 7 0.34 24.3
8-258161 mdo-miR-12324a-3p 100.000 11 0 0 3 13 11 1 2.0 22.3
9-226514 cpo-miR-1379-5p 100.000 12 0 0 2 13 18 7 0.36 24.3
10-214759 oni-miR-10971 100.000 11 0 0 16 26 8 18 1.8 22.3
==> /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/MirGene-BLASTn-eval_10.outfmt6 <==
1-2039267 Tca-Mir-87-P2_3p 100.000 11 0 0 5 15 13 3 0.54 22.3
2-1218024 Pma-Mir-96-P3o2_5p 100.000 11 0 0 16 26 9 19 0.78 22.3
3-551889 Pma-Mir-96-P3o2_5p 100.000 11 0 0 16 26 9 19 0.78 22.3
4-472935 Dno-Mir-1271_5p 100.000 9 0 0 1 9 21 13 9.1 18.3
6-292862 Mml-Mir-2114_5p 100.000 10 0 0 13 22 11 20 2.0 20.3
7-292012 Mml-Mir-2114_5p 100.000 10 0 0 13 22 11 20 2.0 20.3
8-258161 Mdo-Mir-7398-P25_3p 100.000 10 0 0 15 24 10 1 2.9 20.3
9-226514 Mml-Mir-2114_5p 100.000 10 0 0 14 23 11 20 2.2 20.3
11-173986 Csc-Mir-10-P2r2_5p 100.000 19 0 0 2 20 3 21 7.12e-06 38.2
12-168146 Gga-Mir-7441_5p 100.000 10 0 0 13 22 3 12 2.6 20.3
-----------------------------------------
4535565 /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/miRBase-BLASTn-eval_10.outfmt6
4285839 /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/10.2-Peve-sRNAseq-BLASTn-31bp-fastp-merged/MirGene-BLASTn-eval_10.outfmt6
8821404 totalThe default e-value results in alignments for all query sequences, which is likely not what we’d expect.
Decreasing the e-value resulted in fewer query alignments, as we’d expect.
For further analysis, we should probably discuss a reasonable e-value to use for filtering.