Filter low quality tiles from fastq files downloaded from SRA
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
• 2,742 views
•
link
updated
by
Biostar
•
written
by
dolevrahat •
•
written
by
dolevrahat •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Mapping FASTQ files of scRNA-seq to reference genome
written by Researcher •
-
What is the best way to compute genetic distances between FASTQ files?
written by mikazon •
-
How to deal with SRA file without .SRA
written by Andy •
-
How to fasterq-dump 10x genomics snATACseq fastq from SRA
written by rintsen.sherpa •
-
freebayes running error on public data
written by anithanagaraj93 •
-
Does .sra.cache file means failed download?
written by Phoenix Mu •
-
Convert colorspace fastq to basespace fastq
written by aflrios •
-
fastq-dump error for restricted data from dbGAP
written by Rashedul Islam
-
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
written by Brian Bushnell
-
fastq-dump error: transfer unknown
written by mufernando •
If those reads are renamed then the tile information is probably lost.
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.
then there's only one way to find out!
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)?
From the SRA, using fastq-dump