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  • Rename fastq seq ID with unique identifier

    Hi everyone,
    I have a problem, my solid data do not have unique identifier and I'm afraid it could be a problem at some point in the analysis.

    I would like to rename every fastq sequence with an unique identifier

    @Indx_1 - @Indx-10000000 etc

    now they are labelled: @1_5_1645_F3

    I'm a newbie in bioinformatics and wanted to try with awk but wasn't sure how to deal with the @ beeing also inside the qualities (in ASCII). And the fastx tool just renumber but do not give the possibility to add an identifier...

    Any ideas?

    Thank

    Have a nice evening

  • #2
    While this can certainly be done with standard awk, bioawk, makes it a bit easier:

    Code:
    awk -c fastx '{printf("@Indx-%d\n%s\n+\n%s\n",cnt++,$seq,$qual)}' old.fastq > new.fastq
    ...on reflection, this isn't too hard using standard awk...

    Code:
    awk '{if( (NR-1)%4 ) print; else printf("@Indx-%d\n",cnt++)}' old.fastq > new.fastq
    ...this depends on the first entry starts on the first line, and following entries occur every four lines after that.

    Comment


    • #3
      Try something like this ...
      cat file.fq | awk '{if ((p%4)==0) print "@whatev_"p;else print $0;p++}'

      If you're repairing paired data, you will lose the pairs. sadly.

      (edit: alex beat me to it)

      Comment

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