I tired running cuffdiff on two RNA samples: Liver & Intestine.
After aligning with tophat, I ran cuffcompare
but my genes file looks like this:
My transcripts* and genes files have the correct gene and transcript names:
Any clues?
After aligning with tophat, I ran cuffcompare
Code:
cuffcompare -o GFF -r ../hg19.RefFlat.GFF3 ../Liver/transcripts.gtf ../Lung/transcripts.gtf
Code:
cuffdiff GFF.combined.gtf ../Liver/accepted_hits.sam ../Lung/accepted_hits.sam
Code:
ref_trans_id class_code gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi ref_id XLOC_000001-[chr22:17517459-17539682] - - - chr22:17517459-17539682 0 0 0 0.56927 0 1.37434 - XLOC_000002-[chr22:17565848-17591387] - - - chr22:17565848-17591387 2.37959 0.696966 4.06222 15.9232 12.1168 19.7296 - XLOC_000003-[chr22:17956627-18033845] - - - chr22:17956627-18033845 0.540063 0 1.16367 0.413014 0 0.889921 - XLOC_000004-[chr22:18043182-18073647] - - - chr22:18043182-18073647 92.8549 79.4174 106.292 1.11535 0 2.40326 - XLOC_000005-[chr22:18121484-18211987] - - - chr22:18121484-18211987 2.41355 0.706914 4.12019 1.38433 0.254029 2.51463 - XLOC_000006-[chr22:18560685-18572206] - - - chr22:18560685-18572206 3.25714 0.953993 5.56028 3.11362 1.1444 5.08285 - XLOC_000007-[chr22:18593558-18614498] - - - chr22:18593558-18614498 3.26743 0.704014 5.83085 0.960786 0 2.17638 - XLOC_000008-[chr22:18632757-18660160] - - - chr22:18632757-18660160 3.48871 0.849702 6.12772 3.43404 1.14438 5.7237 - XLOC_000009-[chr22:18893735-18899600] - - - chr22:18893735-18899600 25.8998 16.5909 35.2086 0 0 0 -
Code:
gene_id bundle_id chr left right FPKM SAMD11 45228 chr1 861120 879961 0.794517 NOC2L 45228 chr1 879583 894679 25.374 ISG15 45228 chr1 948846 949915 3.06525 AGRN 45228 chr1 955502 991492 8.73339 C1orf159 45228 chr1 1017197 1051736 1.44667 SDF4 45228 chr1 1152288 1167447 89.863 UBE2J2 45228 chr1 1189293 1209234 12.5814 ACAP3 45228 chr1 1227763 1243269 5.66814 PUSL1 45228 chr1 1243993 1247056 2.45665
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