Running cufflinks

[oxydeepu]

Hi,

I have a doubt regarding running cufflinks. i have to seperate tophat
output i need to get combined cufflinks result for this two tophat
outputs. i ran

cufflinks accepted_hits_1.bam accepted_hits_2.bam -o output

Or should i do by concatenating two output files from tophat and run for a
consolidated file.??

Will this make a difference.?
Please help.??
Thank you in advance.

Deepak

[kasutubh]

Hi Deepak,

I don't quite understand what you need to do. Can you be a bit more clear? If you need to get a combined cufflinks result what you can do is the following,

cufflinks -o output -G (reference file) accepted_hits.bam accepted_hits.bam

Hope this helps,

[pbluescript]

The cuffmerge tool is used for merging cufflinks output from numerous bam files. Have you tried that?

[oxydeepu]

Hi,

@Kaustubh: i have done the same as you suggested. i just want an assurance that it will work fine.
@pbluescript: No i havent tried cuffmerge. Can you please help me how to do it..??

[pbluescript]

Hi,

@Kaustubh: i have done the same as you suggested. i just want an assurance that it will work fine.
@pbluescript: No i havent tried cuffmerge. Can you please help me how to do it..??

Not much to it really. Check out the manual:

http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge