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
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM
Comment