FastX Collapser and duplicate removal

Question

[seta]

Hi all,

I don't work with FastX collapse, but I read that it combines identical reads to a single read and keeps count of the reads. However, I didn't understand its meaning from "keeps count of the read". Could you please a bit explain to me? if it meant the program show the count of reads in, for example, in the header of the single read or keeps in the memory or what else?

Thanks

[GenoMax]

I would suggest the you switch to clumpify.sh from BBMap suite. You can dedupe the data and it will keep a count of duplicate reads in the header of the deduplicated file (count=).

[seta]

Thanks, genomax2 for your suggestion. I don't want to use FastX collapser now, just to understand what it does. Please kindly tell me if it also shows a count of reads in the header of the single (deduplicated) reads?

[GenoMax]

Should be easy enough to test. Sorry I have not used fastx-toolkit for a few years now.