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
/galaxy-repl/main/files/006/853/dataset_6853120.dat
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
Mervyn
Dr. Mervyn G Thomas
BSc, MBChB, PhD
Academic Foundation
Doctor
School of Medicine
University of
Leicester
UK