Cuffdiff Error With Mouse Mm9 Genome Reference

Question

[newDNASeqer]

I'm trying to run cuffdiff with mouse_ucsc_mm9 genome reference, but encountered the following error

Loading reference annotation and sequence. No fasta index found for /usr/local/bowtie_indicies/mouse_ucsc_mm9.gtf. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length!

The tophat/cuffliks/cuffmerge steps worked pretty well, I do not understand why cuffdiff throws errors about the genome reference. Does this mean I need to build the index of mm9? if so, what tools can I use? thanks

Answer 1

[Devon Ryan]

You misspecified the command. You gave the annotation where you should have given the reference (it should be

cuffdiff -b reference.fa annotation.gtf groupA1.bam,groupA2.bam... groupB1.bam,groupB2.bam...

or something like that, rather than

cuffdiff -b annotation.gtf groupA1.bam,groupA2.bam... groupB1.bam,groupB2.bam

which is probably more like what you typed).

[nalandaatmi]

Dear Devon,

I need a help on this "Question: Cuffdiff terminated after GffObj::getSpliced() error" question. Will you be able to check this link Cuffdiff terminated after GffObj::getSpliced() error?