Question: Rna-Seq Preprocessing Before De-Novo Transcriptome Assembly ?
2
gravatar for Nicolas Rosewick
7.2 years ago by
Belgium, Brussels
Nicolas Rosewick7.5k wrote:

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.

assembly rna transcriptome • 3.5k views
ADD COMMENTlink written 7.2 years ago by Nicolas Rosewick7.5k
2
gravatar for Mikael Huss
7.2 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Mikael Huss4.6k
1

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.

ADD REPLYlink written 7.2 years ago by Sameet290
1
gravatar for Rm
7.2 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:
  1. Filter for low quality sequences;

  2. Duplicate read removal

  3. Error filtering

ADD COMMENTlink written 7.2 years ago by Rm7.8k
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