RNA-Seq: tuxedo suite transcription start site identification

[zillerm]

Hi,

I am using the most recent version of the tuxedo tools, particularly cufflinks and cummeRbund for RNA-Seq data analysis. I was wondering how you can extract the coordinates of all identified TSS from the cuffdiff output?
Thank you very much,
Best
Michael

[Charitra]

I am also trying to find TSS in my cuffdiff data

Hi,

I am using the most recent version of the tuxedo tools, particularly cufflinks and cummeRbund for RNA-Seq data analysis. I was wondering how you can extract the coordinates of all identified TSS from the cuffdiff output?
Thank you very much,
Best
Michael

[sdriscoll]

I'm pretty sure you will have to fish that out of the GTF file you used for differential testing in Ciffdiff.