How to use cxb files from cuffquant in cuffdiff?

Question

[pedereri]

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

[pedereri]

Ok thanks for that..I am running it now...(taking a long time)

[Sukhi Singh]

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.

[pedereri]

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?

[Sukhi Singh]

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.

[pedereri]

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?

Answer 1

[Sukhi Singh]

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]

[tikshyadav19]

i too found same problem as we did processed data using cuffquant do any one had idea how to proceed with cuff_quant.cxb