For loop to go over all files in a folder to execute bwa mem

Question

[ravigenomeinfo]

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 :)

[Pierre Lindenbaum]

everyone am mem Hello working to i bwa with take a few minutes to write the rights tags please....

Answer 1

[Pierre Lindenbaum]

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.

[ravigenomeinfo]

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

[5heikki]

Did you write your script in Windows? $'\r' sounds like a Microsoft style linebreak. Run dos2unix yourScript.sh and then try again