trim 3' adapter sequence for mRNA-Seq?

[slny]

Hi,

Should I trim 3' adapter sequence for mRNA-Seq? Why?

Thanks,
Slny

[shurjo]

Not sure what you mean by 3' adapter here as the adapter for most mRNA-Seq protocols is the same at both ends of the ds cDNA.

[slny]

Actually any adapter. I just wonder whether I need to trim adapter sequences from the reads for mRNA Seq.

[shurjo]

Under normal circumstances no trimming should be needed as the adapters are not part of the read (they contain the binding sites for the sequencing primers, hence the actual read starts after the adapter). Some people filter the raw data for reads arising from adapter dimers, but that issue is seperate from your question about trimming the reads.

HTH,

Shurjo

[slny]

Very good explanation. Thanks.

[steven]

Yes, thanks Shurjo, this makes sense.
Still, slny, you may be interested in having a look at SeqTrim.

[slny]

Thanks a lot. It's a very good paper.

[volks]

when your sequencing reads are longer than the fragments of your library (which are usually somewhat normally distributed), then you should do 3' trimming.

i recommend cutadapt cutadapt.

[slny]

Thanks, volks. It's a very useful tool for small non-coding RNA studies.

[slny]

steven, can SeqTrim take fastq file as input files? I didn't find any input option for fastq format.

[steven]

Looks like quality values have to be provided separately (http://www.scbi.uma.es/bio/soft/seqt...TrimReadme.pdf). Feel free to contact the authors -I am not one of them .

[volks]

Thanks, volks. It's a very useful tool for small non-coding RNA studies.

yes. but also useful for RNAseq and genomic sequencing. give it a try.

[slny]

Thanks a lot for all the responses. The suggestions helped me a lot.

[steven]

A new one: Btrim. Check also this thread.

[slny]

Thanks a lot, steven.