Thank you so much for this! I will give it a try and hopefully be able to complete cuffdiff after this!
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Still stuck at 99%
Mallela,
Unfortunately, it appears that my cuffdiff run is stuck at 99% again. I performed the markduplicates run just fine for all of my samples, then ran through cufflinks and cuffmerge with the new reads. I allowed cuffdiff to run overnight and it has stopped at the same point that it was stuck at yesterday. Do you have any other recommendations?
LaurenComment
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how about you try inserting this extra option into your picard command ?
Code:REMOVE_DUPLICATES=true
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Btw, can you paste me your recent cuffdiff command that you have used after you have marked the duplicates? Did you use the *_md.bam files?Originally posted by mallela View Posthow about you try inserting this extra option into your picard command ?
Code:REMOVE_DUPLICATES=true
Why don't you try using cuffquant on your *_md.bam files and then use the cuffdiff on the resultant *.cxb files ? The cufflinks site says that it will speed up the process.Comment
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