Cufflinks Output

Question

[abn4]

Hi,

i have run cufflinks for my Bam files to look after the FPKM values and i got the output.

later i took the output transcripts.gtf file and converted into bedgraph file to view in UCSC genome browser,but i got different fpkm values for same location

what should i do with them?should i sum up?is there any script or any tool that i can use it(just for saving the time)

here is the sample bedgraph file

track type=bedGraph name=s6 visibility=full color=255,0,0

chr1 11874 12227 0.0000000000
chr1 11874 12227 0.0286938296
chr1 11874 12227 0.1072298182
chr1 11874 14409 0.0000000000
chr1 11874 14409 0.0286938296
chr1 11874 14409 0.1072298182
chr1 12595 12721 0.0000000000
chr1 12613 12721 0.1072298182
chr1 12646 12697 0.0286938296

Thank you

Answer 1

[JC]

Cufflinks is reporting isoforms with overlapping exons, did you use gene models (Ensembl | UCSC knownGenes) in your analysis?

[abn4]

yes i did use the GTF file from the UCSC browser.