Question: Cufflinks Help
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Thomas, Mervyn G. (Dr.) • 10 wrote:
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
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modified 5.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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5.1 years ago by
Thomas, Mervyn G. (Dr.) • 10
