best method for splicing variant analysis if I have the counts already?
2
0
Entering edit mode
3.2 years ago
decppced • 0

Hello everybody.

I am new in coding and RNA-analysis, so please bear with me. I am trying to find some package (and pipeline if possible) to run an analysis to find the differentially expressed isoforms between my conditions. I already have the counts of all the isoforms and the annotations. What is the best tool for this?

I have found that EdgeR can deal with splicing variants but it needs the sequence and exons; but as I said, I already have the isoform counts so I don't need to go back in steps. Any idea?

Thanks

Bioconductor RNA-seq splicinganalysis isoform • 1.5k views
ADD COMMENT
3
Entering edit mode
3.2 years ago
ashish ▴ 680

You can try DRIMSeq for differential transcript usage. If you can get hold of the raw data and restart the analysis QoRTs -> JunctionSeq is the way to go.

ADD COMMENT
0
Entering edit mode

Can DRIMSeq handle the already counted isoforms? Thanks

ADD REPLY
1
Entering edit mode

Yes it can, check out the vignette

ADD REPLY
0
Entering edit mode

Awesome, thanks so much!

ADD REPLY
0
Entering edit mode
3.2 years ago

If you already have the counts isoforms why would you need exon information?

Typically you would need the splicing information (junctions/exons) to be able to assign counts to an isoform. But if you already have the information you can move onto the statistical analysis. The statistical analysis does not need the splicing information.

ADD COMMENT
0
Entering edit mode

you are right, that is what I am saying, I have all that and I don't want to go back to that using packages that ask me to work with raw data. I want something that can deal with the counts of the isoforms which is what I have right now. I hope I made myself clear this time. Any suggestions? thanks again

ADD REPLY

Login before adding your answer.

Traffic: 1427 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