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How to rename multiple fastq files

Hello,

I have several fastq files like this:

7097-TK273759-HiSeqShotgun_S9_R1_001.fastq.gz
7097-TK273759-HiSeqShotgun_S9_R2_001.fastq.gz
7097-TK273763-HiSeqShotgun_S10_R1_001.fastq.gz
7097-TK273763-HiSeqShotgun_S10_R2_001.fastq.gz
7097-TK273775_1-HiSeqShotgun_S14_R1_001.fastq.gz
7097-TK273775_1-HiSeqShotgun_S14_R2_001.fastq.gz
7097-TK273775_2-HiSeqShotgun_S15_R1_001.fastq.gz
7097-TK273775_2-HiSeqShotgun_S15_R2_001.fastq.gz

I want to rename like this:

TK273759_R1.fastq.gz
TK273759_R2.fastq.gz
TK273763_R1.fastq.gz
TK273763_R2.fastq.gz
TK273775_1_R1.fastq.gz
TK273775_1_R2.fastq.gz
TK273775_2_R1.fastq.gz
TK273775_2_R2.fastq.gz
fastq
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updated by Ram Ram • written by neha.jnu463 • neha.jnu463

3 answers

use brename

brename -p ".+(TK[0-9]+_?[12]?)-HiSeq.+(_R[12])_.+fastq.gz" -r '$1$2.fastq.gz' -d
• 0 views • link
written by Ming Tommy Tang Ming Tommy Tang

try below code in terminal:

for file in *.fastq.gz; do
    if [[ $file =~ 7097-([^-]+)-HiSeqShotgun_(S[0-9]+)_R([0-9]+)_001.fastq.gz ]]; then
        prefix="${BASH_REMATCH[1]}_R${BASH_REMATCH[3]}"
        suffix=".fastq.gz"
        mv "$file" "${prefix}${suffix}"
    fi
done

enter image description here

• 0 views • link
written by Sajad • Sajad

The code you provided worked! I really apprecaite your help.

• 0 views • link
written by neha.jnu463 • neha.jnu463

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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written by Ram Ram

Renaming multiple files at once is something that comes up quite often. That's why it's better to be acquainted with tools that have such feature. Most of these renaming tasks are one of a kind so writing scripts and regexes might become cumbersome compare to creating a vim macro.

Terminal based file managers like nnn or ranger have a bulk renaming feature where you can edit the list of file names in your preferred editor like vim.

Also in emacs dired mode you can make your buffer writable and rename your files all at once.

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written by barslmn • barslmn

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