#!/bin/bash ## Job Name #SBATCH --job-name=cg-spur ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=4-12:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/033021-roslin-spur # Load Python Mox module for Python module availability module load intel-python3_2017 source /gscratch/srlab/programs/scripts/paths.sh /gscratch/srlab/programs/ncbi-blast-2.10.1+/bin/blastx \ -query /gscratch/srlab/sr320/data/cg/rna.fna \ -db /gscratch/srlab/sr320/blastdb/ProteinsSpur5.0 \ -out /gscratch/scrubbed/sr320/033021-roslin-spur/CgRNA-blastx-spur.tab \ -num_threads 40 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt "6 qaccver saccver evalue"
Tag Archives: SBATCH
-job-name=cg-spur
#!/bin/bash ## Job Name #SBATCH --job-name=cg-spur ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=4-12:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/032621-roslin-spur # Load Python Mox module for Python module availability module load intel-python3_2017 source /gscratch/srlab/programs/scripts/paths.sh /gscratch/srlab/programs/ncbi-blast-2.10.1+/bin/blastx \ -query /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/cgigas_uk_roslin_v1_genomic-mito.fa \ -db /gscratch/srlab/sr320/blastdb/ProteinsSpur5.0 \ -out /gscratch/scrubbed/sr320/032621-roslin-spur/Cg-blastx-spur.tab \ -num_threads 40 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt "6 qaccver saccver evalue"
job-name=ron-rosM
#!/bin/bash ## Job Name #SBATCH --job-name=ron-rosM ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=15-00:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/030521-ronrosM # Directories and programs bismark_dir="/gscratch/srlab/programs/Bismark-0.21.0" bowtie2_dir="/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" reads_dir="/gscratch/srlab/sr320/data/cg/" genome_folder="/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/" source /gscratch/srlab/programs/scripts/paths.sh ${bismark_dir}/bismark_genome_preparation \ --verbose \ --parallel 28 \ --path_to_aligner ${bowtie2_dir} \ ${genome_folder} #/zr3644_11_R2.fastp-trim.20201206.fq.gz find ${reads_dir}*_R1.fastp-trim.20201202.fq.gz \ | xargs basename -s _R1.fastp-trim.20201202.fq.gz | xargs -I{} ${bismark_dir}/bismark \ --path_to_bowtie ${bowtie2_dir} \ -genome ${genome_folder} \ -p 8 \ -score_min L,0,-0.6 \ --non_directional \ -1 ${reads_dir}{}_R1.fastp-trim.20201202.fq.gz \ -2 ${reads_dir}{}_R2.fastp-trim.20201202.fq.gz \ find *.bam | \ xargs basename -s .bam | \ xargs -I{} ${bismark_dir}/deduplicate_bismark \ --bam \ --paired \ {}.bam ${bismark_dir}/bismark_methylation_extractor \ --bedGraph --counts --scaffolds \ --multicore 28 \ --buffer_size 75% \ *deduplicated.bam # Bismark processing report ${bismark_dir}/bismark2report #Bismark summary report ${bismark_dir}/bismark2summary #run multiqc /gscratch/srlab/programs/anaconda3/bin/multiqc . # Sort files for methylkit and IGV find *deduplicated.bam | \ xargs basename -s .bam | \ xargs -I{} ${samtools} \ sort --threads 28 {}.bam \ -o {}.sorted.bam # Index sorted files for IGV # The "-@ 16" below specifies number of CPU threads to use. find *.sorted.bam | \ xargs basename -s .sorted.bam | \ xargs -I{} ${samtools} \ index -@ 28 {}.sorted.bam find *deduplicated.bismark.cov.gz \ | xargs basename -s _bismark_bt2_pe.deduplicated.bismark.cov.gz \ | xargs -I{} ${bismark_dir}/coverage2cytosine \ --genome_folder ${genome_folder} \ -o {} \ --merge_CpG \ --zero_based \ {}_bismark_bt2_pe.deduplicated.bismark.cov.gz #creating bedgraphs post merge for f in *merged_CpG_evidence.cov do STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 10) {print $1, $2, $3, $4}}' \ > "${STEM}"_10x.bedgraph done for f in *merged_CpG_evidence.cov do STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 5) {print $1, $2, $3, $4}}' \ > "${STEM}"_5x.bedgraph done #creating tab files with raw count for glms for f in *merged_CpG_evidence.cov do STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 10) {print $1, $2, $3, $4, $5, $6}}' \ > "${STEM}"_10x.tab done for f in *merged_CpG_evidence.cov do STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 5) {print $1, $2, $3, $4, $5, $6}}' \ > "${STEM}"_5x.tab done
job-name=hw-bsnlP
#!/bin/bash ## Job Name #SBATCH --job-name=hw-bsnlP ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/021921-hw-bsnP # Directories and programs bismark_dir="/gscratch/srlab/programs/Bismark-0.21.0" bowtie2_dir="/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" reads_dir="/gscratch/srlab/sr320/data/cg/" genome_folder="/gscratch/srlab/sr320/data/Cgig-genome/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/" source /gscratch/srlab/programs/scripts/paths.sh #${bismark_dir}/bismark_genome_preparation \ #--verbose \ #--parallel 28 \ #--path_to_aligner ${bowtie2_dir} \ #${genome_folder} #/zr3644_11_R2.fastp-trim.20201206.fq.gz find ${reads_dir}*_R1.fastp-trim.20201206.fq.gz \ | xargs basename -s _R1.fastp-trim.20201206.fq.gz | xargs -n 1 -P 6 -I{} ${bismark_dir}/bismark \ --path_to_bowtie ${bowtie2_dir} \ -genome ${genome_folder} \ -p 4 \ --non_directional \ -1 ${reads_dir}{}_R1.fastp-trim.20201206.fq.gz \ -2 ${reads_dir}{}_R2.fastp-trim.20201206.fq.gz \ find *.bam | \ xargs basename -s .bam | \ xargs -I{} ${bismark_dir}/deduplicate_bismark \ --bam \ --paired \ {}.bam ${bismark_dir}/bismark_methylation_extractor \ --bedGraph --counts --scaffolds \ --multicore 14 \ --buffer_size 75% \ *deduplicated.bam # Bismark processing report ${bismark_dir}/bismark2report #Bismark summary report ${bismark_dir}/bismark2summary # Sort files for methylkit and IGV find *deduplicated.bam | \ xargs basename -s .bam | \ xargs -I{} ${samtools} \ sort --threads 28 {}.bam \ -o {}.sorted.bam # Index sorted files for IGV # The "-@ 16" below specifies number of CPU threads to use. find *.sorted.bam | \ xargs basename -s .sorted.bam | \ xargs -I{} ${samtools} \ index -@ 28 {}.sorted.bam
job-name=hw-bs
#!/bin/bash ## Job Name #SBATCH --job-name=hw-bs ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=20-00:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/021321-hw-bs # Directories and programs bismark_dir="/gscratch/srlab/programs/Bismark-0.21.0" bowtie2_dir="/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" reads_dir="/gscratch/srlab/sr320/data/cg/" genome_folder="/gscratch/srlab/sr320/data/Cgig-genome/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/" source /gscratch/srlab/programs/scripts/paths.sh #${bismark_dir}/bismark_genome_preparation \ #--verbose \ #--parallel 28 \ #--path_to_aligner ${bowtie2_dir} \ #${genome_folder} #/zr3644_11_R2.fastp-trim.20201206.fq.gz find ${reads_dir}*_R1.fastp-trim.20201206.fq.gz \ | xargs basename -s _R1.fastp-trim.20201206.fq.gz | xargs -I{} ${bismark_dir}/bismark \ --path_to_bowtie ${bowtie2_dir} \ -genome ${genome_folder} \ -p 4 \ -score_min L,0,-0.6 \ --non_directional \ -1 ${reads_dir}{}_R1.fastp-trim.20201206.fq.gz \ -2 ${reads_dir}{}_R2.fastp-trim.20201206.fq.gz \ find *.bam | \ xargs basename -s .bam | \ xargs -I{} ${bismark_dir}/deduplicate_bismark \ --bam \ --paired \ {}.bam ${bismark_dir}/bismark_methylation_extractor \ --bedGraph --counts --scaffolds \ --multicore 14 \ --buffer_size 75% \ *deduplicated.bam # Bismark processing report ${bismark_dir}/bismark2report #Bismark summary report ${bismark_dir}/bismark2summary # Sort files for methylkit and IGV find *deduplicated.bam | \ xargs basename -s .bam | \ xargs -I{} ${samtools} \ sort --threads 28 {}.bam \ -o {}.sorted.bam # Index sorted files for IGV # The "-@ 16" below specifies number of CPU threads to use. find *.sorted.bam | \ xargs basename -s .sorted.bam | \ xargs -I{} ${samtools} \ index -@ 28 {}.sorted.bam # # # find *deduplicated.bismark.cov.gz \ # | xargs basename -s _R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz \ # | xargs -I{} ${bismark_dir}/coverage2cytosine \ # --genome_folder ${genome_folder} \ # -o {} \ # --merge_CpG \ # --zero_based \ # {}_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz # # # #creating bedgraphs post merge # # for f in *merged_CpG_evidence.cov # do # STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) # cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 10) {print $1, $2, $3, $4}}' \ # > "${STEM}"_10x.bedgraph # done # # # # for f in *merged_CpG_evidence.cov # do # STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) # cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 5) {print $1, $2, $3, $4}}' \ # > "${STEM}"_5x.bedgraph # done # # # #creating tab files with raw count for glms # # for f in *merged_CpG_evidence.cov # do # STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) # cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 10) {print $1, $2, $3, $4, $5, $6}}' \ # > "${STEM}"_10x.tab # done # # # for f in *merged_CpG_evidence.cov # do # STEM=$(basename "${f}" .CpG_report.merged_CpG_evidence.cov) # cat "${f}" | awk -F $'\t' 'BEGIN {OFS = FS} {if ($5+$6 >= 5) {print $1, $2, $3, $4, $5, $6}}' \ # > "${STEM}"_5x.tab # done
job-name=cg-spur
#!/bin/bash ## Job Name #SBATCH --job-name=cg-spur ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=4-12:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/021321-cgig-spur # Load Python Mox module for Python module availability module load intel-python3_2017 source /gscratch/srlab/programs/scripts/paths.sh /gscratch/srlab/programs/ncbi-blast-2.10.1+/bin/blastx \ -query /gscratch/srlab/sr320/data/cg/GCF_000297895.1_oyster_v9_cds_from_genomic.fna \ -db /gscratch/srlab/sr320/blastdb/ProteinsSpur5.0 \ -out /gscratch/scrubbed/sr320/021321-cgig-spur/Cg-blastx-spur.tab \ -num_threads 40 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt "6 qaccver saccver evalue"
Mox Job – blastx
#!/bin/bash ## Job Name #SBATCH --job-name=blasts ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=0-12:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/020821-cgig-sp # Load Python Mox module for Python module availability module load intel-python3_2017 source /gscratch/srlab/programs/scripts/paths.sh /gscratch/srlab/programs/ncbi-blast-2.8.1+/bin/blastx \ -query /gscratch/srlab/sr320/data/cg/GCF_000297895.1_oyster_v9_cds_from_genomic.fna \ -db /gscratch/srlab/blastdbs/UniProtKB_20190109/uniprot_sprot.fasta \ -out /gscratch/scrubbed/sr320/020821-cgig-sp/Cg-blastx-sp.tab \ -evalue 1E-05 \ -num_threads 40 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt "6 qaccver saccver evalue"
[code]#!/bin/bash ## Job Name #SBATCH...
#!/bin/bash ## Job Name #SBATCH --job-name=re-duck ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=30-00:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/1217/ # Directories and programs bismark_dir="/gscratch/srlab/programs/Bismark-0.21.0" bowtie2_dir="/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" reads_dir="/gscratch/srlab/strigg/data/Pgenr/FASTQS/" genome_folder="/gscratch/srlab/sr320/data/geoduck/v01/" source /gscratch/srlab/programs/scripts/paths.sh ${bismark_dir}/bismark_genome_preparation \ --verbose \ --parallel 28 \ --path_to_aligner ${bowtie2_dir} \ ${genome_folder} find ${reads_dir}*_R1_001_val_1.fq.gz \ | xargs basename -s _R1_001_val_1.fq.gz | xargs -I{} ${bismark_dir}/bismark \ --path_to_bowtie ${bowtie2_dir} \ -genome /gscratch/srlab/sr320/data/geoduck/v01 \ -p 4 \ -score_min L,0,-0.6 \ -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/{}_R1_001_val_1.fq.gz \ -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/{}_R2_001_val_2.fq.gz \ find *.bam | \ xargs basename -s .bam | \ xargs -I{} ${bismark_dir}/deduplicate_bismark \ --bam \ --paired \ {}.bam ${bismark_dir}/bismark_methylation_extractor \ --bedGraph --counts --scaffolds \ --multicore 14 \ --buffer_size 75% \ *deduplicated.bam # Bismark processing report ${bismark_dir}/bismark2report #Bismark summary report ${bismark_dir}/bismark2summary # Sort files for methylkit and IGV find *deduplicated.bam | \ xargs basename -s .bam | \ xargs -I{} ${samtools} \ sort --threads 28 {}.bam \ -o {}.sorted.bam # Index sorted files for IGV # The "-@ 16" below specifies number of CPU threads to use. find *.sorted.bam | \ xargs basename -s .sorted.bam | \ xargs -I{} ${samtools} \ index -@ 28 {}.sorted.bam find *deduplicated.bismark.cov.gz \ | xargs basename -s _R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz \ | xargs -I{} ${bismark_dir}/coverage2cytosine \ --genome_folder ${genome_folder} \ -o {} \ --merge_CpG \ --zero_based \ {}_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
[code]#!/bin/bash ## Job Name #SBATCH...
#!/bin/bash ## Job Name #SBATCH --job-name=el_01 ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=3-12:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/1117c/ # Eleni 20191107 # The purpose of this script is to align fastq files to a genome, and output the # alignments as bam files, whose mapping quality is greater than 30. # to run this script, place in same folder as the files you want to move and write ./bowtie2_cluster.sh in terminal source /gscratch/srlab/programs/scripts/paths.sh find /gscratch/scrubbed/sr320/eleni/*.fq | xargs basename -s .fq | xargs -I{} bowtie2 \ -x /gscratch/scrubbed/sr320/eleni/GCA_900700415 \ -U /gscratch/scrubbed/sr320/eleni/{}.fq \ -p 28 \ -S /gscratch/scrubbed/sr320/1117c/{}.sam find /gscratch/scrubbed/sr320/1117/*.sam | \ xargs basename -s .sam | \ xargs -I{} /gscratch/srlab/programs/samtools-1.9/samtools \ view -b -q 30 /gscratch/scrubbed/sr320/1117c/{}.sam -o /gscratch/scrubbed/sr320/1117c/{}.bam #for file in $files #do #echo ${file} # print the filename to terminal screen #bowtie2 -q -x GCA_900700415 -U ${file}.fq|samtools view -b -q 30 > ${file}.bam #conduct the alignment and output the file #done #Explanation of terms: #bowtie2 -q -x <bt2-idx> -U <r> -S <sam> #-q query input files are in fastq format #-x <bt2-idx> Indexed "reference genome" filename prefix (minus trailing .X.bt2). #-U <r> Files with unpaired reads. # The default of bowtie2, is to write the output of the alignment to the terminal. # Also, bowtie does not write BAM files directly, but SAM output can be converted to BAM on the fly by piping bowtie's output to samtools view. # samtools options # -b output BAM # -q <integer> : discards reads whose mapping quality is below this number #for file in $files #do #echo ${file} # print the filename to terminal screen #bowtie2 -q -x GCA_900700415 -U ${file}.fq|samtools view -b -q 30 > ${file}.bam #conduct the alignment and output the file #done
bowtie
#!/bin/bash ## Job Name #SBATCH --job-name=el_01 ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=3-12:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/sr320/1117c/ # Eleni 20191107 # The purpose of this script is to align fastq files to a genome, and output the # alignments as bam files, whose mapping quality is greater than 30. # to run this script, place in same folder as the files you want to move and write ./bowtie2_cluster.sh in terminal source /gscratch/srlab/programs/scripts/paths.sh find /gscratch/scrubbed/sr320/eleni/*.fq | xargs basename -s .fq | xargs -I{} bowtie2 \ -x /gscratch/scrubbed/sr320/eleni/GCA_900700415 \ -U /gscratch/scrubbed/sr320/eleni/{}.fq \ -p 28 \ -S /gscratch/scrubbed/sr320/1117c/{}.sam find /gscratch/scrubbed/sr320/1117/*.sam | \ xargs basename -s .sam | \ xargs -I{} /gscratch/srlab/programs/samtools-1.9/samtools \ view -b -q 30 /gscratch/scrubbed/sr320/1117c/{}.sam -o /gscratch/scrubbed/sr320/1117c/{}.bam #for file in $files #do #echo ${file} # print the filename to terminal screen #bowtie2 -q -x GCA_900700415 -U ${file}.fq|samtools view -b -q 30 > ${file}.bam #conduct the alignment and output the file #done #Explanation of terms: #bowtie2 -q -x <bt2-idx> -U <r> -S <sam> #-q query input files are in fastq format #-x <bt2-idx> Indexed "reference genome" filename prefix (minus trailing .X.bt2). #-U <r> Files with unpaired reads. # The default of bowtie2, is to write the output of the alignment to the terminal. # Also, bowtie does not write BAM files directly, but SAM output can be converted to BAM on the fly by piping bowtie's output to samtools view. # samtools options # -b output BAM # -q <integer> : discards reads whose mapping quality is below this number #for file in $files #do #echo ${file} # print the filename to terminal screen #bowtie2 -q -x GCA_900700415 -U ${file}.fq|samtools view -b -q 30 > ${file}.bam #conduct the alignment and output the file #done