Rna seq Denovo assembly

Question

[anitha.b]

Hi,

I want to run rna seq, but there is no reference that's why i m trying to run trinity. The problem is, trinity takes all the samples for assembly, but my data is large so can i take some samples and run trinity is possible? if yes what is the criteria for selecting samples to run trinity..

Thank you, Anitha

[Mehmet]

Hi,

If you want to make a de novo transcriptome assembly, you should use all reads. concanate all right and left reads as all.reads.right.fq, and all.reads.left.fq, then use them for data preprocess. (quality control, trimming etc.)

Answer 1

[aniruddhapandit]

Once you have created the concatenated files and have trimmed all the adaptor sequences, etc (Trimmomatic, Cutadapt), remember to use the normalisation script which comes along with the Trinity Suite. This will help in chopping down the data to a very workable size. Hope this helps.

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Insilico-Normalization