Hi All,
I'm having a weird issue with the output from cuffcompare, and I wondered if anyone had seen the same.
We are using cuffcompare to comapre and track transcripts build from an RNAseq project. We use the following commandline to run cuffcompare:
cuffcompare
According to the cuffcompare manual, cuffcompare is supposed to output a <outprefix>.stats file. We never get this file, although usually we do get the stats in a file name just <outprefix> (e.g. in this case example.cuffcompare). However, this only happens when there are 6 samples or fewer. If we use 7 or more samples, not stats are output anywhere that we can find.
I'm running cuffcompare 2.0.2 using precompiled binaries on 64bit linux. But i've tried with 2.0.0, 1.4.0 and 1.3.0. Same result each time.
Anyone else seen this? We'd really quite like the stats as our pipeline uses them for quality control.
Cheers,
Ian
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I'm having a weird issue with the output from cuffcompare, and I wondered if anyone had seen the same.
We are using cuffcompare to comapre and track transcripts build from an RNAseq project. We use the following commandline to run cuffcompare:
cuffcompare
Code:
cuffcompare -o example.cuffcompare -s /ifs/mirror/genomes/bowtie/hg19.fa -r <( gunzip < refcoding.gtf.gz) ./ctmpL7zs9K/example1.gtf.gz ./ctmpL7zs9K/example2.gtf.gz &> example.cuffcompare.log
I'm running cuffcompare 2.0.2 using precompiled binaries on 64bit linux. But i've tried with 2.0.0, 1.4.0 and 1.3.0. Same result each time.
Anyone else seen this? We'd really quite like the stats as our pipeline uses them for quality control.
Cheers,
Ian
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