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Cuffdiff Error With Mouse Mm9 Genome Reference

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

cuffdiff
• 4,186 views • link
updated by Devon Ryan Devon Ryan • written by newDNASeqer newDNASeqer

1 answer

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).

• 112 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

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