Question: Differential expression analysis at transcript isoform level
0
gravatar for seta
4.4 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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

ADD COMMENTlink modified 4.4 years ago by EVR570 • written 4.4 years ago by seta1.2k
2
gravatar for geek_y
4.4 years ago by
geek_y10k
Barcelona
geek_y10k wrote:

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. 

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by geek_y10k
1
gravatar for EVR
4.4 years ago by
EVR570
Earth
EVR570 wrote:

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

 

ADD COMMENTlink written 4.4 years ago by EVR570
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1186 users visited in the last hour