Hello All,
I have an RNA-Seq pipeline, using the STAR aligner and Cufflinks.
I am running cufflinks in the 'Reference Annotation Based Transcript' assemvbly mode to predict alternative splicing variants.
I have been using Cufflinks on our compute servers for a while now, and I didn't have any problems until recently.
For the past few weeks, Cufflinks always hangs after a few hours of running.
I can't seem to identify the problem. It doesn't seem to be a network issue, as I have installed cufflinks locally and also have the data locally.
I have tried this with cufflinks 2.2.1 and 2.1.1, and both hang. Using STAR version 2.4.0f1.
The only error I get is associated with the STAR output (and I didn't have this problem before either)
Why do I get this error even though I have specified the correct parameters for STAR?
Could this be the reason Cufflinks is hanging?
Thank you!
I have an RNA-Seq pipeline, using the STAR aligner and Cufflinks.
I am running cufflinks in the 'Reference Annotation Based Transcript' assemvbly mode to predict alternative splicing variants.
I have been using Cufflinks on our compute servers for a while now, and I didn't have any problems until recently.
For the past few weeks, Cufflinks always hangs after a few hours of running.
I can't seem to identify the problem. It doesn't seem to be a network issue, as I have installed cufflinks locally and also have the data locally.
I have tried this with cufflinks 2.2.1 and 2.1.1, and both hang. Using STAR version 2.4.0f1.
The only error I get is associated with the STAR output (and I didn't have this problem before either)
BAM record error: found spliced alignment without XS attribute
I find it strange because I do specify the '--outSAMstrandField intronMotif' parameter for STAR.Why do I get this error even though I have specified the correct parameters for STAR?
Could this be the reason Cufflinks is hanging?
Thank you!
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