Question: Differential quantification of splice junction
0
gravatar for Anil Kesarwani
4.3 years ago by
United States
Anil Kesarwani80 wrote:

Hi,

From TopHat 2 alignment, I have obtained outputs containg splice junctions and the corresponding read counts. I am interested in calculating differential splice junction usage between wild type and mutant samples.

In a recent publication (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358997/ ), the DEXSeq function called "testForDEURT" was used to quantify differential splice junction usage between two samples. However, I am not able to figure out the important steps to use this function.

I have wild type and mutant samples in replicates, and therefire some statistics, for example, p-value and FDR, will be needed to define signficantly candidates.

Could somebody please guide me doing this analysis. Any response is highly appreciated.

 

rna-seq dexseq • 1.4k views
ADD COMMENTlink modified 4.3 years ago by SES8.2k • written 4.3 years ago by Anil Kesarwani80

The only actual important steps that are different from the normal DEXSeq workflow are (1) filtering the splice site counts (they mention the filter used in the methods) and (2) annotating splice sites with gene information to allow parsing by DEXseq. You'll have to write something to do (2). (1) can likely be done with awk.

ADD REPLYlink written 4.3 years ago by Devon Ryan91k

To me, the implementaiton of DEXSeq to calculate differential splice junction usage is not straightforward. Could you please explain me in more detail. I managed to prepare my read count (for splice junctions) file in the format of DEXSeq, but I am not able to figure out how the corresponding GTF file should be prepared.

 

ADD REPLYlink written 4.3 years ago by Anil Kesarwani80
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