RNAseq: should I trim both 3' and 5'?
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4.0 years ago
fr ▴ 210

I'm running an RNAseq analysis that was sequenced in Illumina HiSeq 2500.

From the reference docs I can see that adapters are 10 bases long, so I guess that's the specification that I should give to Trim Galore.

I'm wondering if I should trim both 3' and 5' ends or just 5' ends? Should I consider the same 10 bases for both if applicable?

Thanks a lot

RNA-Seq • 2.0k views
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In Illumina sequencing adapter contamination should never be on 5'-end of the read unless you have plain primer dimers with no inserts or you are doing something unusual/custom.

Also take a look at this blog post from authors of FastQC.This is what you will likely find next.

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4.0 years ago

Don't just trim off 20 bases from the end like that. That's stupid, most reads don't have problems with adapters.

For starters, you can use fastqc to see if adapters are a real problem for your samples (ignore the other things fastqc tells you, most of them are not relevant to RNASeq)

If you have an adapter problem, use a trimming program to just remove the adapter sequence. You know that bcl2fastq can do this, so your fastqs might already be trimmed.

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