input of cummerbund

Question

[dimitrischat]

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?

[Santosh Anand]

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

[dimitrischat]

ok thank you. i will read it through

Answer 1

[e.rempel]

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.

[dimitrischat]

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?