Cufflinks stuck in processing locus

Question

[kaktust.uni]

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

Answer 1

[Rox]

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

[kaktust.uni]

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

Answer 2

[sushanthadusumilli]

Any solution found for this issue? I came across same problem on specific files. Please link or mention the possible solutions. Thank You

[colindaven]

It's really, really, really old software. I wouldn't use it. For RNA-seq try an R DESeq2 pipeline (google tutorial), or for transcript discovery try Stringtie as above.