Cuffdiff Question

Question: Cuffdiff Question

5.0 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, The transcript name when using RefSeq as a reference annotation is the "NM_" type of identifier. If you want to include a gene symbol, then the reference annotation should include the attribute "gene_name". The iGenomes GTF files are an example of datasets that include this attribute. http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See: /Example/?/*RNA-seq analysis*/*tools* http://cufflinks.cbcb.umd.edu/faq.html#gtfs http://cufflinks.cbcb.umd.edu/igenomes.html http://cufflinks.cbcb.umd.edu/manual.html (search on page for "gene_name" to see where can be used/output) Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org

rna-seq cufflinks • 794 views

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modified 5.0 years ago by clare Hardman • 20 • written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

5.0 years ago by

clare Hardman • 20

clare Hardman • 20 wrote:

Hello, Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be! Best wishes Clare

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5.0 years ago by

clare Hardman • 20

clare Hardman • 20 wrote:

Hi Noa, Yes I did use Cufflinks so this sounds just like my problem. So how have you dealt with the problem? Best wishes, Clare

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5.0 years ago by

Noa.sher • 10

Noa.sher • 10 wrote:

Dont use the - b parameter Sent from my iPhone; please excuse any brevity or typos!

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