Help with bowtie2 aligning PE Radseq sequences to reference genome

Question

[imda]

Hello all, I have in a folder Radseq paired-end sequences from 300 plants. I am trying to align those PE sequences in loop mode to the reference genome but I have not had success. Could you help me? This is de loop command that I am using for this but it does not work

for f in /home/icruz/data/CGSGH190527-RAD/prueba/*.fq; do bowtie2 -x tic_ref_prueba -1 ${f}_1.fq -2 ${f}_2.fq --threads 30 -S ${f%\.*}_reads_aligned.sam; done

The name of my samples is like:

Teo_1.fq ---> forward

Teo_2.fq ---> reverse

Teo21_1.fq

Teo21_2.fq

Teo3_1.fq

Teo3_2.fq

And so on.....

Best regards

Ivan

[Pierre Lindenbaum]

I am trying to align those PE sequences in loop

use a workflow manager like snakemake or nextflow.