Question: input of cummerbund
0
gravatar for dimitrischat
4 months ago by
dimitrischat40
dimitrischat40 wrote:

Hello all. I finally ran cuffdiff successfully, but now i wanna run cummeRbund on galaxy. i have no idea which of the outputs i must use. do i have to do something now or i had to put an option when cuffdiff ran so i had a specific output for cummeRbund?

rna-seq • 215 views
ADD COMMENTlink modified 4 months ago by e.rempel540 • written 4 months ago by dimitrischat40

see http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

ADD REPLYlink modified 4 months ago • written 4 months ago by Santosh Anand3.0k

ok thank you. i will read it through

ADD REPLYlink modified 4 months ago • written 4 months ago by dimitrischat40
2
gravatar for e.rempel
4 months ago by
e.rempel540
Germany, Heidelberg, COS
e.rempel540 wrote:

Hi,

there is a button in Galaxy UI "Generate SQLite" (default is "NO" !) for CuffDiff tool. Select "Yes", then CuffDiff will generate a SQLite output ready to be used as an only input for CummerBund.

ADD COMMENTlink written 4 months ago by e.rempel540

is there an option for that in the command line ? because i (prefer) ran cuffdiff in terminal. many thanks

edit: or manipulate yourself the output(s) of cuffdiff to make an sqlite file?

ADD REPLYlink modified 4 months ago • written 4 months ago by dimitrischat40
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