Sort Fastq Files...

Question

[znra1]

Does anyone have a utility or pointers to sort fastq files based on the quality value?

TiA, Nash

[Arun]

Just to be sure, by sorting you mean, reads with best average quality should be on the top of the list? Rather, what is your criteria for sorting? And by sorting, do you mean no filtering?

Answer 1

[Istvan Albert]

I assume that you wish to sort the reads by average quality. This could be done easily with Heng Li's bioawk like so:

cat test.fq | awk -c fastx ' { print meanqual($seq),$name,$seq,$qual} ' | sort -k 1 -rn | awk ' { printf("@%s\n%s\n+\n%s\n",$2,$3,$4) } ' > sorted.fq

[Arun]

(+1) got to read bioawk! :)

[Istvan Albert]

bioawk the awesomest tool that rocks the hardest

[Vikas Bansal]

bioawk looks really good. Is there any manual for this? I found some description here

[Istvan Albert]

I wrote a mini help here: https://github.com/ialbert/bioawk/blob/master/README.bio.rst

[Vikas Bansal]

Thanks a lot. Good to know.

Answer 2

[znra1]

Thanks Istvan...but it looks like there might be a typo somewhere? awk on my Ubuntu 12.04 LST doesn't seem to recognize the -c option??

Nash

[Istvan Albert]

you should post this as a comment and you will need to install bioawk and run that!

[znra1]

Ok....thanks. I just tried make from your tar file, but it looks like this Ubuntu non-developer distribution really needs a lot of basic unix libs and tools (I had to get lex and yacc first!). Any idea where I can get zlib.h to compile addon.c please? Sorry for the inconvenience...

[Istvan Albert]

try this link: http://bcc.bx.psu.edu/courses/597D-2011/getting-started.html#using-linux