Filter low quality tiles from fastq files downloaded from SRA

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6.8 years ago

dolevrahat ▴ 40

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

fastq quality filtering SRA • 2.0k views

ADD COMMENT • link updated 6.7 years ago by Biostar 20 • written 6.8 years ago by dolevrahat ▴ 40

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

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k

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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.

ADD REPLY • link 6.8 years ago by dolevrahat ▴ 40

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then there's only one way to find out!

ADD REPLY • link 6.8 years ago by BioinfGuru ★ 2.1k

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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)?