Question: Should I retain ORFs predicted on minus strand of transcripts which assembled from strand-specific RNA-seq ?
0
gravatar for sckinta
4.4 years ago by
sckinta550
United States
sckinta550 wrote:

Hi, 

I assembled a transcriptome using Trinity with  setting of --SS_lib_type R, then I continued to predict ORFs using TransDecoder. The final result gives me 236711 ORFs with 202113 on + strand of transcripts. This is a good sign to show strand-specific setting worked. but I am not sure whether I should retain those ~ 20000 ORFs predicted on - strand.

I will further do DE analysis and SNP calling. Will retaining those minus-strand ORF affect my following analysis?

Thank you,

Chun

ADD COMMENTlink written 4.4 years ago by sckinta550
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1693 users visited in the last hour