Is it better to use a merged transcriptome or the reference annotation for RSEM gene expression
2
0
Entering edit mode
15 months ago

Just wondering if it is better to use a merged transcriptome of the samples I have or should I use the human reference annotation? I intend to do differential expression so I was planning on using RSEM to calculate counts. I know that the merged transcriptome might result in novel transcripts but I was wondering if it still would be a fair analysis to just use the human reference annotation?

rsem gene_expression RNA-Seq • 426 views
ADD COMMENT
1
Entering edit mode
15 months ago
JC 12k

Depends if you want to check only known genes/transcripts or you want to consider the presence of new unknown transcripts/isoforms. From the research point of view you want to do both, then compare the differences and see if there are any advantages from one annotation to the other.

ADD COMMENT
1
Entering edit mode
15 months ago

For human, the reference annotation should be better than what you could work out experimentally. So if you aren't looking for novel transcripts, just use the annotation that already exists.

ADD COMMENT

Login before adding your answer.

Traffic: 2502 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