Thank you so much for this! I will give it a try and hopefully be able to complete cuffdiff after this!
-
-
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
-
how about you try inserting this extra option into your picard command ?
Code:REMOVE_DUPLICATES=true
Comment
-
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
-
The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
Comment