Hi!
I have been using cufflinks, then cuffcompare to analyze my RNAseq data (6 samples) via Galaxy. i used the Ensembl bovine genome as reference (UMD3.1.75.gtf)
Cuffcompare produces two refmap files as expected (for the first two samples), but I noticed that the sizes of the two refmap files are very different: approximately 1.6Mb/20000 lines for the first one (sample A), 120kb/2000 lines for the second (sample B).
Isn't this unexpected/abnormal?
The cufflinks gtf files used as input in cuffcompare are of similar size (80Mb) for all 6 samples.
When I switch the order in the analysis, it produces the opposite result: larger refmap file for sample B, smaller file for sample A --> ???
Can you comment on that? Am I missing something obvious? (very possible, it is my first RNAseq analysis).
rdt
I have been using cufflinks, then cuffcompare to analyze my RNAseq data (6 samples) via Galaxy. i used the Ensembl bovine genome as reference (UMD3.1.75.gtf)
Cuffcompare produces two refmap files as expected (for the first two samples), but I noticed that the sizes of the two refmap files are very different: approximately 1.6Mb/20000 lines for the first one (sample A), 120kb/2000 lines for the second (sample B).
Isn't this unexpected/abnormal?
The cufflinks gtf files used as input in cuffcompare are of similar size (80Mb) for all 6 samples.
When I switch the order in the analysis, it produces the opposite result: larger refmap file for sample B, smaller file for sample A --> ???
Can you comment on that? Am I missing something obvious? (very possible, it is my first RNAseq analysis).
rdt