Question: How many input BAM files for Cuffquant?
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gravatar for wmorgan
3.3 years ago by
wmorgan0
United States
wmorgan0 wrote:

I'm trying to use the Cufflinks v. >2.2.0 workflow, which uses Cuffquant. The Cufflinks documentation says that "Cuffquant takes as input a single SAM/BAM file of aligned reads and a single GTF/GFF file of gene annotations." However, running Cuffquant at usegalaxy.org gives the option to add replicates, so I added the BAM files of my replicates (e.g., three for the control samples). Cuffquant ran fine for both the control and experimental, but when I tried to use the two .cxb output files in Cuffdiff, I got a warning that "No conditions are replicated...", indicating that Cuffdiff didn't recognize that replicates were entered into Cuffquant. So should I run Cuffquant with each BAM file from Tophat separately?

cufflinks cuffquant • 2.3k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by wmorgan0
0
gravatar for wmorgan
3.3 years ago by
wmorgan0
United States
wmorgan0 wrote:

Looking at the bottom of usegalaxy.org's Cuffquant tool page, I just noticed that the instructions conflict with the Cufflinks documentation (see my original question). According to usegalaxy.org:

Input format

Cuffquant takes Cufflinks or Cuffcompare GTF files as input along with two or more SAM files containing the fragment alignments for two or more samples.

Any advice?

ADD COMMENTlink written 3.3 years ago by wmorgan0
0
gravatar for wmorgan
3.3 years ago by
wmorgan0
United States
wmorgan0 wrote:

Follow this link to see the response on this issue: A: CUffDIFF fatal exit code Error 139

 

ADD COMMENTlink written 3.3 years ago by wmorgan0
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