cuffcompare - FPKM==0

Boel

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Join Date: Oct 2009

Posts: 62
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cuffcompare - FPKM==0

02-25-2010, 05:45 AM

Dear All,

I am using TopHat and Cufflinks to look at RNA seq data from 4 lanes on paired end data. After running cuffcompare, most (~95%) of my FPKM values are zero in the transcript.tmap files, even though the confidence intervals are not:

THOC1 ENST00000261600 i CUFF.168011 CUFF.168011.0 100 0.000000 0.000000 5.524216 1.892857 112 CUFF.168011.0
THOC1 ENST00000261600 o CUFF.168003 CUFF.168003.0 100 91.833304 63.824409 119.842199 37.700000 60 CUFF.168003.0
THOC1 ENST00000261600 i CUFF.168014 CUFF.168014.0 100 0.000000 24.039246 43.550817 27.939560 182 CUFF.168014.0
THOC1 ENST00000261600 i CUFF.168017 CUFF.168017.0 100 0.000000 23.307955 44.481971 27.012903 155 CUFF.168017.0
THOC1 ENST00000261600 i CUFF.168020 CUFF.168020.0 100 0.000000 1.819694 10.605954 5.139394 165 CUFF.168020.0
THOC1 ENST00000261600 i CUFF.168023 CUFF.168023.0 100 0.000000 34.336648 81.714214 24.000000 53 CUFF.168023.0
THOC1 ENST00000261600 e CUFF.168026 CUFF.168026.0 100 0.000000 38.204817 87.516951 26.000000 53 CUFF.168026.0
THOC1 ENST00000261600 e CUFF.168029 CUFF.168029.0 100 0.000000 0.000000 4.871750 1.669291 127 CUFF.168029.0
- - u CUFF.168032 CUFF.168032.0 100 0.000000 7.537617 22.612852 12.080882 136 CUFF.168032.0
TYMS ENST00000323250 c CUFF.168035 CUFF.168035.0 100 0.000000 3.270622 14.526530 6.625000 144 CUFF.168035.0
TYMS ENST00000323224 c CUFF.168038 CUFF.168038.0 100 0.000000 5.665085 33.018536 8.000000 53 CUFF.168038.0
TYMS ENST00000323250 i CUFF.168041 CUFF.168041.0 100 0.000000 9.303752 23.713787 13.656442 163 CUFF.168041.0
TYMS ENST00000323250 i CUFF.168044 CUFF.168044.0 100 0.000000 1.294351 12.812750 5.834862 109 CUFF.168044.0
TYMS ENST00000323250 i CUFF.168047 CUFF.168047.0 100 0.000000 8.012186 23.107405 12.871429 140 CUFF.168047.0

Cuffcompare was run like this:
cuffcompare -o ./cuffC/100224ref -r Homo_sapiens.exon.chr.NCBI36.48_1.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

Using cufflinks-0.8.1, tophat-1.0.12, bowtie-0.12.1. The reference GTF file was collected from ensembl and reformatted (added "chr", removed all lines except exons).

The transcripts.gtf files all have FPKM values.

Any idea of what could have gone wrong?

Thank you,
Boel
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