Remove contamination reads from fastq files

Question

[tsomakiank]

Hello! I am trying to analyze some Rna-seq data and the qc of the raw reads indicate that there is some kind of contamination going on. Is there any tool I can use to remove these reads?

Thanks in advance!

Answer 1

[GenoMax]

If you have a reference genome available for the sample then you can align the data (using an aligner) and then extract reads that align to the genome leaving contamination behind.

[tsomakiank]

Can I somehow do that if I am aligning to a transcriptome?

[GenoMax]

Within the limits of short read technology (assuming you have illumina data) and way aligners work. Aligners will try to align the read as best as they can so there is a chance that you may end up getting some reads that do not belong. You could use more stringent alignment settings to reduce that chance.

[tsomakiank]

Thanks a lot GenoMax!