Hi
I am trying to first use the cuffquant tool before using cuffdiff, but when I try to use the cxb files from cuffquant in cuffdiff I get this error message:
Error: cuffdiff requires at least 2 SAM files
I read that it was possible to use the cuffquant files in cuffdiff, but there is no examples anywhere that I can find....
Here is my code (minus the directories)
./cuffdiff -b /ppatens3.fa -N -L "case","control" -o "./diff_quant" --multi-read-correct case/abundances.cxb control/abundances.cxb
Thanks
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written
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pedereri •
A transcript gtf file is an important non-optional parameter. Provide that for your reference genome, the error will go away.
cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam]
i too found same problem as we did processed data using cuffquant do any one had idea how to proceed with cuff_quant.cxb
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Ok thanks for that..I am running it now...(taking a long time)
It can take 2-5 hours depending upon the species, sample sequencing depth and the number of cores your are using.
Use comments to write something thats not an answer.
Well I got to "Testing for differential expression and regulation in locus" and then the process was killed after 8%....
Could it be that my computer is not powerful enough?
It might not be memory, people have experienced it before as well. If you can't find anything try their google group
https://groups.google.com/forum/#!forum/tuxedo-tools-users and for good, post back the answer so other know what happened.
Well I found this link
https://groups.google.com/forum/#%21searchin/tuxedo-tools-users/cuffdiff$20killed/tuxedo-tools-users/6c8U6-eJ2sg/mjeu1FltdioJ
But it doesn't really help. There wasn't any fix. Is there another link that you are thinking of?