Question: Cufflinks stuck in processing locus
0
gravatar for kaktust.uni
27 days 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 27 days ago by Roxane Boyer310 • written 27 days ago by kaktust.uni10
2
gravatar for Roxane Boyer
27 days ago by
Roxane Boyer310
France/Marseille/IBDM
Roxane Boyer310 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 27 days ago • written 27 days ago by Roxane Boyer310
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 27 days ago by kaktust.uni10
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