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Davide Degli Esposti • 80 wrote:
Dear Galaxy team,
I have a question about RNA analysis with the cufflinks package.
I have some bam files to analyze from a SOLiD platform. Some previous
tests show that these bam/sam files are different from those coming
from Tophat and cufflinks cannot assemble them using a reference
annotation (XS attribute lacking in spliced alignments). (see
https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-
datasetscufflinks). An apparent solution is to include the reference
annotation in the cuffmerge (see https://main.g2.bx.psu.edu/u/davide-
degliesposti/h/rna-seqtest-datasetsapril-20132) or cuffcompare (see
https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-
datasetsjan-2013-1) steps. Doing like this allowed me to run cuffdiff
on my datasets without apparent technical errors. However, when I
compare the list of differentially expressed transcripts (DETs), these
results extremely different: using cuffcompare, I got 390 DETs and
using cuffmerge I got 770 DETs, but just 60 genes are shared between
the two lists. The parameters used in cuffdiff (FDR, Min Alignement
counts, etc.) are the same for the two analyses.
Do you have any explanation about that? I expected that cuffcompare
and cuffmerge did not lead to outputs quantitatively different. Where
may the source of this difference be?
I thank you for your cooperation
Davide
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International Agency for Research on Cancer
Tel. +33 4 72738036
Fax. +33 4 72738322
150, cours Albert Thomas
69372 Lyon Cedex 08
France
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modified 5.7 years ago
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Jeremy Goecks • 2.2k
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5.7 years ago by
Davide Degli Esposti • 80
