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!
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!
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