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Rna-Seq Preprocessing Before De-Novo Transcriptome Assembly ?

Hi,

Which type of preprocessing do I have to performe on my reads before doing a de-novo transcriptome assembly (Trinity) ? My data comes from a Illumina GAII plateform (paired-end 2x72 bp). Do I have to trim the 3' adapter sequence ?

Thanks a lot,

N.

rna transcriptome assembly
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updated by Rm Rm • written by Nicolas Rosewick Nicolas Rosewick

2 answers

If you think that you have 3' adapter sequences in the reads, you should trim them off. This should mainly happen if you have sequenced miRNAs or other short transcripts.

I would also recommend quality trimming before de novo assembly.

• 10 views • link
written by Mikael Huss Mikael Huss

This is correct, your first step would be removal of the 3' adapters, followed by quality trimming. This will also mostly trim something from the 3' ends of the read. You probably should also do fastqc as a norm so that you know your data in general is in good standing.

• 16 views • link
written by Sameet • Sameet

  1. Filter for low quality sequences;

  2. Duplicate read removal

  3. Error filtering

• 17 views • link
written by Rm Rm

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