Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: CuffDiff Hangs at same point
0
gravatar for Lauren Laboissonniere
2.6 years ago by
Lauren Laboissonniere • 20
Iowa State University
Lauren Laboissonniere • 20 wrote:

Hi all,

I am currently encountering errors with CuffDiff because it appears to be stuck at the same locus for the past 48 hours and I was wondering if anyone else had this problem or had found a solution?

Here is my cuffdiff command line: cuffdiff -o diff_out -b index_mouse.fa -p 8 -L M1,M2 merged_asm/merged.gtf ./M1_1_3.th/accepted_hits.bam,./M1_2_13.th/accepted_hits.bam,./M1_2_14.th/accepted_hits.bam,./M1_2_15.th/accepted_hits.bam,./M1_2_17.th/accepted_hits.bam ./M2_1_2.th/accepted_hits.bam,./M2_2_8.th/accepted_hits.bam,./M2_2_23.th/accepted_hits.bam,./M2_2_24.th/accepted_hits.bam,./M2_2_26.th/accepted_hits.bam

The point where this command is stuck is under "Testing for differential expression and regulation in locus".

Thanks!

Lauren
rna-seq cufflinks cuffdiff • 623 views
ADD COMMENT • link •
modified 2.6 years ago • written 2.6 years ago by Lauren Laboissonniere • 20
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I personally don't know of a specific known cause for this as a tool problem/error (suspect it is instead a content issue of some type that is triggering a compute-intensive cycle: region/s with many splices, fragmented assembly, etc), but you may have more luck with a post over at the general Biostars forum (this one is for Galaxy): https://www.biostars.org

I would suggest sharing a bit more about your data content when posting there. If you don't, will probably be asked to and this would help to attract constructive replies.

Take care, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Lauren Laboissonniere
2.6 years ago by
Lauren Laboissonniere • 20
Iowa State University
Lauren Laboissonniere • 20 wrote:

Thank you!

ADD COMMENT • link written 2.6 years ago by Lauren Laboissonniere • 20
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 174 users visited in the last hour