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Whats the best way to deal with paired end reads of different lengths when using cuffdiff? I have multiple runs at different lengths for the same treatment that I want to compare to another treatment.
thanks!
thanks!
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Is there anyway to do this? Cuffdiff is a great tool and it would especially useful for this project. Maybe I should clarify that the distance between the mate pairs is what is different within and across treatments, not read length. I would expect that treating the reads as single end would be a great waste of valuable information. Has anyone tried to use the output from Cuffcompare (parse the isoform levels from the .tracking file?) to deal with this or is there a way to convince cuffdiff to do it?
Many thanks!
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