Differential expression analysis at transcript isoform level

Question

[seta]

Hi everybody,

I would like to know how I can do differential expression analysis at the transcript isoform level, assuming gene A as a differential expressed gene has 4 transcript isoforms (say, ENST00000339847, ENST00000417570, ENST00000547437, ENST00000551730), how to figure out which transcript is differentially expressed?

Thanks

Answer 1

[GouthamAtla]

You need to use programs like tuxedo-suite or StringTie that estimates transcript level abundances and DE transcripts.

Basic pipeline would be to use a splice aware aligner like STAR or TopHat2 and input the resulting bam files to cufflinks/cuffdiff or StringTie to get DE transcripts.

STAR is super fast than tophat2 but before using it you should read about the compatibility of STAR output with the cuffdiff/StringTie as these programs requires a specific flag for reads aligned in a spliced manner.

Answer 2

[EVR]

Hi,

Try Trinity pipeline, with that you can find the differential expression for isoforms as well as gene level. Here is the link: http://trinityrnaseq.github.io/#Downstream_analyses