Hello Bao,
The best test is to examine some of the assembled transcripts and
compare them to known gene clusters (your reference GTF) and see which
threshold produces the best match. Even if you are using a custom
genome, and there is no reference annotation for this data, Trackster
could be used to visualize the data and some homology searches to
closely related organisms could let you know if you are on the right
track (or including spurious transcripts or excluding valid transcripts).
The cufflinks/compare/diff documentation can help explain FPKM (there
are many factors considered):
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
If you do get stuck, contacting the tool authors is the next step:
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results
Take care,
Jen
Galaxy team
On 3/29/12 8:14 AM, vang0...@umn.edu wrote:
Dear all,
I changed the minimum alignment count to: 100, 400, and 1000
minimum alignment differential expressed genes
100 4, 000
400 2,000
1000 (default) 1,000
I was wondering, which minimum alignment we should go with? It would appear
the higher the alignment, the amount of differential expressed genes are
decreased.
I was also wondering if the minimum alignment refers to the # of reads per
sequence? Is this true?
Also how are the FPKM and the minimum alignment are related?
Thanks,
Bao
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The Galaxy User list should be used for the discussion of
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