Hi All,

I am trying to analyse some human RNA-seq dataset which is in BAM format to 
generate FPKM values using cufflinks. The ensembl group have aligned the data 
using BWA 0.5.9 to generate these BAM datasets. I realise that TopHat 
alignments are optimal for Cufflinks, but is it possible for me to use 
cufflinks or some other tool to derive FPKM values from BWA aligned reads?

I tried using cufflinks on one of the BAM files but got an error:
Error running cufflinks.
return code = -11
Command line:
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 
The additional output was:
cufflinks v2.1.1
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8

I have sent it to the galaxy team and awaiting their reply. Any thoughts about 
how I can go about analysing this data.

Best wishes


Dr. Mervyn G Thomas BSc, MBChB, PhD
Academic Foundation Doctor
School of Medicine
University of Leicester
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