Trimming by fastp for multiple PE fastq.gz files using shell script

Dear all,

I was trying to do trimming using fastp for multiple paired end fastq files with the help of a shell script. The two (forward and reverse) fastq.gz files were formed by SRA toolkit using fastq-dump.

fastq-dump -I --split-files --gzip

When I try to run the two files for analysis by fastp I am unable to specify the two paired end files inside my shell script. I tried

for file1 in /path_to_files/*_1.fastq.gz
do
  file2=${file1%%_1.fastq.gz }"_2.fastq.gz"
  fastp -i ${file1} -I ${file2} -o ${file1}_trimmed.fastq.gz -O ${file2}_trimmed.fastq.gz
done

but it gives an error:

Error to read gzip file ............... the file doesn't exist.

I don't know where I am doing wrong and is there any alternative way to specify my two files one by one in a for loop in bash shell for multiple files.

Any help will be much appreciated. Thanks!

shell fastp rna-seq bash

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updated 2.6 years ago by juditlamar •

• written 7.7 years ago by Mithil Gaikwad •

3 answers

assuming sorting the paths will return the correct output:

$ find src/test/resources/ -name "*.fq.gz" | sort | paste - - | while read A B ; do echo " fastq1 and is  $A fastq2 is $B" ; done

 fastq1 and is  src/test/resources/S1.R1.fq.gz fastq2 is src/test/resources/S1.R2.fq.gz
 fastq1 and is  src/test/resources/S2.R1.fq.gz fastq2 is src/test/resources/S2.R2.fq.gz
 fastq1 and is  src/test/resources/S3.R1.fq.gz fastq2 is src/test/resources/S3.R2.fq.gz
 fastq1 and is  src/test/resources/S4.R1.fq.gz fastq2 is src/test/resources/S4.R2.fq.gz
 fastq1 and is  src/test/resources/S5.R1.fq.gz fastq2 is src/test/resources/S5.R2.fq.gz

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written 7.7 years ago by Pierre Lindenbaum

Assume all your data follow the same format:

for first in `ls *_1.fastq.gz`;
do
    second=`echo ${first} | sed 's/_1/_2/g'`
    fastp -i ${first} -I ${second} -o ${first}_trimmed.fastq.gz -O ${second}_trimmed.fastq.gz
done

• 0 views • link

written 2.6 years ago by DareDevil

Gather feedback from users and stakeholders to identify areas for improvement. Plan for regular updates and iterations to add new features, enhance existing functionality, and address user feedback.

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written 2.6 years ago by juditlamar •