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
Jen Galaxy team
On 3/29/12 8:14 AM, firstname.lastname@example.org wrote:
I changed the minimum alignment count to: 100, 400, and 1000
minimum alignment differential expressed genes 100 4, 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?
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