How to Write Loop For Trimming Every FastQ File Individually

1

I have human Rna-Seq data by reading nanopore. Data has over 1000 .fastq files. I want to trim all fastq files individually. I am using NanoFilt for trimming. All Fastq files are in the directory(not gzip format).

How can I write a loop or command line for trimming all fastq files individually?

I am using Linux Ubuntu 21.04.


Trimming


Nanopore


Fastq


Rna-Seq

• 97 views

Hello, this is a rather basic question. You could start by googling something like "bash loop files directory" to get plenty of examples on how to write loops in bash. The basic structure of the loop is probably going to be something like this:

for file in $directory; do
    echo $file
    <nanofilt cmd> $file
done

Then if you run into specific issues, feel free to come back and ask for more direction.


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