need help with script for hisat2 alignment

Question

[Antonio.Aubry]

Hello all,

I'm new to bioinformatics and programming in general so apologies if this comes off as naive.

I am working with the data set that comes with "Transcript-level expression analysis on RNA-seq experiments with HISAT, stringtie and Ballgown" Pertea et al. 2016. Instead of writing the same command over and over as in the paper, I am trying to write a for loop to iterate over the samples. Below is my script:

#!/bin/bash
set -e

###
SAMPLES=chrX_data/files.txt

##Store bam files in this directory
mkdir -p sam
#### number of CPUs
CPUS=8

####reference genome
IDX=chrX_data/indexes/chrX_tran

for SAMPLE in $(cat $SAMPLES)
do
    R1=samples/${SAMPLE}_chrX_1.fastq
    R2=samples/${SAMPLE}_chrX_2.fastq
    SAM=${SAMPLE}_chrX.sam

    hisat2 -p $CPUS --dta -x $IDX -1 $R1 -2 $R2 -S $SAM
done

However, when I run this I get the following error

Warning: Could not open read file "samples/ERR188044_chrX_1.fastq" for reading; skipping...Error: No input read files were valid

Any help would be greatly appreciated

[Antonio.Aubry]

I actually just figured it out, but can't figure out how to delete the post. Sorry!

[Istvan Albert]

A more appropriate course of action is to follow up with the answer, and with that, you can help someone else that may run into a similar problem. That's the entire purpose of the site. Imagine if every post with a solution would be deleted.

[Antonio.Aubry]

Got it. Thanks......

Answer 1

[GenoMax]

Are you running this from a location which has samples directory (with actual samples) in it? That path appears to be incorrect. Should samples be chrX_data instead in the script?

[Antonio.Aubry]

You're correct the path was incorrectt