Rename fastq seq ID with unique identifier

454rocks · 03-28-2012, 12:24 PM

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

Alex Renwick · 03-28-2012, 01:24 PM

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.

Richard Finney · 03-28-2012, 01:29 PM

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)

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03-28-2012, 12:24 PM	#1
454rocks Junior Member Location: Switzerland Join Date: Sep 2011 Posts: 2	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

03-28-2012, 01:24 PM	#2
Alex Renwick Member Location: Houston, Texas Join Date: Jul 2011 Posts: 44	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.

03-28-2012, 01:29 PM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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)