Question: Rna seq Denovo assembly
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gravatar for anitha.b
6 weeks ago by
anitha.b0
anitha.b0 wrote:

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

ADD COMMENTlink modified 6 weeks ago by aniruddhapandit0 • written 6 weeks ago by anitha.b0

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.)

ADD REPLYlink written 6 weeks ago by Mehmet230
0
gravatar for aniruddhapandit
6 weeks ago by
aniruddhapandit0 wrote:

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

ADD COMMENTlink written 6 weeks ago by aniruddhapandit0
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