Question: Cuffdiff Error- empty output files URGENT
gravatar for Lindsay44
2.3 years ago by
Lindsay440 wrote:


I am trying to run Cuffdiff, but it doesn't seem to be working. When I run the script, the following message comes up:

You are using Cufflinks v2.2.1, which is the most recent release.

And then it stops running and produces empty output files.

Why is this happening?

I tried sorting the SAM files a few different ways, but that doesn't seem to help. What SAMtools command should I be using to convert and sort the files (I used HiSat2 for alignment)?

Also, do I need to use Cufflinks to assemble the transcriptome? A file in the correct format was included in the reference genome download.

Thank you. Please respond ASAP.

rna-seq cufflinks samtools • 658 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Lindsay440

You need to run Cufflinks on your aligned bam files, then use cuffmerge to merge all of the "assembled transcripts" (cufflinks output file) and then run cuffdiff on the cuffmerge file and adding in the aligned bam. files.

ADD REPLYlink written 2.3 years ago by VY120

I did that. It is still producing empty output files.

ADD REPLYlink written 2.3 years ago by Lindsay440
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