I ran 2 x 50GB SAM files that had been generated by TopHat 1.0.14 through the pre-release Cufflinks 0.8.4 using -G and a UCSC hg19 GTF annotation file:
cufflinks -p10 -G /gtf_files/hg19_UCSC.gtf accepted_hits.sam
Then through Cuffcompare 0.8.4:
cuffcompare -r /gtf_files/hg19_UCSC.gtf /normal/transcripts.gtf /cancer/transcripts.gtf
Then through Cuffdiff 0.8.4:
cuffdiff -p14 stdout.combined.gtf /normal/tophat_out/accepted_hits.sam /cancer/tophat_out/accepted_hits.sam
No problems encountered.
Thanks Cole for the fix and making the pre-release version of Cufflinks available.
Chris
cufflinks -p10 -G /gtf_files/hg19_UCSC.gtf accepted_hits.sam
Then through Cuffcompare 0.8.4:
cuffcompare -r /gtf_files/hg19_UCSC.gtf /normal/transcripts.gtf /cancer/transcripts.gtf
Then through Cuffdiff 0.8.4:
cuffdiff -p14 stdout.combined.gtf /normal/tophat_out/accepted_hits.sam /cancer/tophat_out/accepted_hits.sam
No problems encountered.
Thanks Cole for the fix and making the pre-release version of Cufflinks available.
Chris
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