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
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 /galaxy-repl/main/files/006/853/dataset_6853120.dat
The additional output was:
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.
Dr. Mervyn G Thomas BSc, MBChB, PhD
Academic Foundation Doctor
School of Medicine
University of Leicester