Should I retain ORFs predicted on minus strand of transcripts which assembled from strand-specific RNA-seq ?
0
1
Entering edit mode
7.3 years ago
sckinta ▴ 690

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

TransDecoder strand-specific RNA-Seq • 2.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 757 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6