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Question: Correct Input Into The Minimum Alignment Count
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gravatar for vang0280@umn.edu
6.7 years ago by
vang0280@umn.edu • 20
vang0280@umn.edu • 20 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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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by vang0280@umn.edu • 20
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gravatar for Jennifer Hillman Jackson
6.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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
ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
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