Rna-Seq Preprocessing Before De-Novo Transcriptome Assembly ?

Question

[Nicolas Rosewick]

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.

Answer 1

[Mikael Huss]

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.

[Sameet]

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.

Answer 2

[Rm]

1. Filter for low quality sequences;

2. Duplicate read removal

3. Error filtering