Filter low quality tiles from fastq files downloaded from SRA

Question

[dolevrahat]

Hello

I am looking for a way to filter low quaility tiles from fastq files downloaded from SRA. I am aware that BBMap has a module called FilterByTile that does exactly that. However the developer state that "Renamed reads (such as those in the SRA) probably won’t work."

Can anyone recommend a similar tool that can parse fastq files obtained from SRA?

Thanks in advance

[WouterDeCoster]

If those reads are renamed then the tile information is probably lost.

[dolevrahat]

I'm not I understand why. This is an example for a read ID from the file: SRR1976450.3 HWI-ST640:627:D26AFACXX:3:1101:1995:2149 As far I understand the sequence 3:1101:1995:2149 correspond to the flowcell lane,tile and X and Y coordinates within the tile. So it appear the information is there.

[BioinfGuru]

then there's only one way to find out!

[WouterDeCoster]

That's indeed not how a fastq renamed by SRA looks like, so you might be lucky. It seems all necessary information is there. From where/how did you download this file(s)?

[dolevrahat]

From the SRA, using fastq-dump