Can Differential Isoform expression analysis can be performed using DESeq2 package
1
0
Entering edit mode
priyanka.m • 0
@03ddb485
Last seen 18 hours ago
India

Hello,

I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential expression of transcripts then performing some downstream manual analysis to find which of the differential transcripts belong to same gene. Or if there is any other R package that can perform DIE analysis by taking in salmon quant files directly.

I know DESeq2 is used for gene-level analysis, I am not sure if it can be extended to transcript level and if there are any underlying parameters I should take into consideration before performing such analysis.

Any advice will be highly appreciated.

Thank you.

RNASeqData isoform DESeq2 • 118 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 5 hours ago
United States

In the Swish paper we show that, while overall the sensitivity and precision are roughly on target for many gene-level tools, for certain classes of transcripts with high inferential uncertainty, we found the Swish method had better control of FDR (1 - precision). See for example Fig 3 where Swish controls error well for the transcripts with highest uncertainty of assignment. To run Swish, you would just need to have run Salmon with --numBootstraps or --numGibbsSamples of 20 or 30. Swish has a DE vignette similar to DESeq2:

https://mikelove.github.io/fishpond/articles/swish.html

ADD COMMENT
0
Entering edit mode

Thank you so much Michael.

Both the paper and links are very useful.

ADD REPLY

Login before adding your answer.

Traffic: 261 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