Question: Cufflinks stuck in processing locus
0
gravatar for kaktust.uni
11 weeks ago by
kaktust.uni10
kaktust.uni10 wrote:

Hi all,

I'm using Cufflinks for my RNAseq data, and for some reason 2 out of 8 samples are stuck during 'Processing Locus' (by stuck meaning its not continuing to write into the output files but still the process/CPU is working) without any apparent reason or an error messages/indication for the problem. I've ran it a few times and it still got stuck in the same position for both samples. all the samples were indexed + aligned the same way using BOWTIE2 and TOPHAT2. the .bam files seem to be OK. the other 6 samples were "Cufflinked" OK.

any Ideas?

Cheers,

TY

ADD COMMENTlink modified 11 weeks ago by Roxane Boyer430 • written 11 weeks ago by kaktust.uni10
2
gravatar for Roxane Boyer
11 weeks ago by
Roxane Boyer430
France/Marseille/IBDM
Roxane Boyer430 wrote:

Hi there,

I actually faced the same issue month ago, I reported the issue here in github : https://github.com/cole-trapnell-lab/cufflinks/issues/72 but as you can see, the issue is still unsolved...

As an alternative, I will suggest to use Stringtie : https://ccb.jhu.edu/software/stringtie/

It is really efficient, way faster than Cufflinks, I have completely adopted the tool.

It is advised to use the aligner hisat2 instead of tophat2, but I think it will work fine.

Hope this helped you !

Cheers,

Roxane

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Roxane Boyer430
1

Thanks Roxane,

I think i'll give cufflinks some more time to run...if it still wont produce outputs i'll consider the alternatives.

Cheers,

TY

ADD REPLYlink written 11 weeks ago by kaktust.uni10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1424 users visited in the last hour