Hello friends !!
Actually I am tiring to execute bwa mem to align my reads to reference genome. Here are the manual command I ma doing
#For 1st sample
cd SRR1
bwa mem -t 20 genome/genomic.fna ./SRR1/good/SRR10176137_1.good.fq ./SRR1/good/SRR10176137_2.good.fq > mappings/SRR10176137.sam
cd ..
# For 2nd sample
cd SRR2
bwa mem -t 20 genome/genomic.fna ./SRR2/good/SRR10176138_1.good.fq ./SRR2/good/SRR10176138_2.good.fq > mappings/SRR10176138.sam
like I have 200 SRR samples so I am trying following code for loop i.e.
my data structure is i.e. = data/SRR......SRR200/good/S_1.fq.
working directory : data list SRR...SRR; mappings; vcf; genome
So each SRR* directory has good directory containing paired sequence .fq files
Here out sam files in data/mapping directory in data directory
#!/bin/bash
for d in SRR*/good; do
cd $d;
# my command
bwa mem -t 40 genome/genomic S*_1.good.fq S*_2.good.fq > ../mappings/*.sam
cd ..
done
Any modification highly appreciated
Thank you :)
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ravigenomeinfo •
For loop to go over all files in a folder to execute bwa mem
this is a good idea, but you'd better use a workflow manager like snakemake or nextflow. If you're not familiar with those tools try to use a simple Makefile. See Parallel for bwa mem - problem with -R argument for ID and SM for an example.
Hi Pierre, thanks for your suggestion. Actually in my code can you please suggest any modification, or correction because it gives me error i.e. command not found i.e. bwa_mem.bash: line 1: $'\r': command not found
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