Comparison of experimental groups in Cufflinks

[ega2d]

Hi all,

I am analyzing Illumina-generated RNAseq data (63bp paired end reads). I have three experimental groups: X, Y, Z. I would like to find the similarities in alternative splicing between X and Z that are NOT present in Y. I am struggling with the best way to accomplish this with the output files from Cufflinks (and cuffdiff). Should I just compare FPKMs for each sample (from the tracking files) or is there a way I could take advantage of the stats run in cuffdiff? Which output file would be the helpful in this situation?

I have successfully run all the parts of my pipeline...It's just that tricky bit of figuring out the best way to visualize/summarize/prioritize the data that's giving me trouble.

I would greatly appreciate any advice, comments, etc. Thanks!

[RockChalkJayhawk]

Hi all,

I am analyzing Illumina-generated RNAseq data (63bp paired end reads). I have three experimental groups: X, Y, Z. I would like to find the similarities in alternative splicing between X and Z that are NOT present in Y. I am struggling with the best way to accomplish this with the output files from Cufflinks (and cuffdiff). Should I just compare FPKMs for each sample (from the tracking files) or is there a way I could take advantage of the stats run in cuffdiff? Which output file would be the helpful in this situation?

I have successfully run all the parts of my pipeline...It's just that tricky bit of figuring out the best way to visualize/summarize/prioritize the data that's giving me trouble.

I would greatly appreciate any advice, comments, etc. Thanks!

This really depends on what ou are looking for. Perhaps the easiest way is to take all of the genes that show up as significant for X, Y, and Z, and run them through a Venn Diagram like Venny.