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Old 06-04-2011, 06:37 PM   #1
slny
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Default trim 3' adapter sequence for mRNA-Seq?

Hi,

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

Thanks,
Slny
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Old 06-04-2011, 06:44 PM   #2
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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.
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Old 06-04-2011, 07:04 PM   #3
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Actually any adapter. I just wonder whether I need to trim adapter sequences from the reads for mRNA Seq.
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Old 06-04-2011, 07:53 PM   #4
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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
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Old 06-05-2011, 03:30 AM   #5
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Very good explanation. Thanks.
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Old 06-07-2011, 01:29 AM   #6
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Yes, thanks Shurjo, this makes sense.
Still, slny, you may be interested in having a look at SeqTrim.
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Old 06-07-2011, 03:04 AM   #7
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Thanks a lot. It's a very good paper.
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Old 06-07-2011, 03:26 AM   #8
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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.
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Old 06-07-2011, 06:29 AM   #9
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Thanks, volks. It's a very useful tool for small non-coding RNA studies.
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Old 06-08-2011, 07:44 AM   #10
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steven, can SeqTrim take fastq file as input files? I didn't find any input option for fastq format.
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Old 06-08-2011, 07:59 AM   #11
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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 .
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Old 06-08-2011, 08:06 AM   #12
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Quote:
Originally Posted by slny View Post
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.
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Old 06-08-2011, 11:32 AM   #13
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Thanks a lot for all the responses. The suggestions helped me a lot.
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Old 06-13-2011, 09:03 AM   #14
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A new one: Btrim. Check also this thread.
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Old 06-14-2011, 06:15 AM   #15
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Thanks a lot, steven.
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