I ran tophat (1.1.0) without a mouse gtf file. Run cufflinks (0.9.1) without a mouse gtf file. Then run cuffcompare with a mouse gtf file and two gtf files generated from cufflinks for my two samples. Finally, I ran cuffdiff with compare.combined.gtf and two accepted_hits.bam files.
However, I checked one of the cuffdiff output files: gene_exp.diff. I found there is still multiple FPKM problem for many genes (see below):
XLOC_000009 Cspp1 chr1:10053629-10189988 q1 q2 OK 44.5012 58.359 0.271096 -2.93789 0.00330457 yes
XLOC_000010 Arfgef1 chr1:10053629-10189988 q1 q2 OK 10.0582 7.68137 -0.269589 4.88261 1.04688e-06 yes
XLOC_000011 Arfgef1 chr1:10053629-10189988 q1 q2 OK 40.66 31.8566 -0.244 17.6406 0 yes
XLOC_000013 Arfgef1 chr1:10053629-10189988 q1 q2 OK 2.7768 40.8059 2.68753 -144.972 0 yes
XLOC_000015 Arfgef1 chr1:10053629-10189988 q1 q2 OK 54.0345 65.0081 0.18489 -12.9339 0 yes
XLOC_000016 Arfgef1 chr1:10053629-10189988 q1 q2 OK 23.4654 43.6672 0.62107 -29.4492 0 yes
XLOC_000031 Tram2 chr1:20986216-20997026 q1 q2 OK 5.8219 2.96147 -0.67594 3.70609 0.000210487 yes
XLOC_000032 Tram2 chr1:20986216-20997026 q1 q2 OK 3.33419 14.9065 1.49757 -29.7646 0 yes
XLOC_000057 Tmem131 chr1:36849038-36996484 q1 q2 OK 37.3723 30.8444 -0.191975 5.03247 4.84195e-07 yes
Did I do something wrong? Wht do some genes only have one FPKM (one row) and some genes have multple FPKM (multple rows)?
I have another question regarding gene_exp.diff file. The first gene Cspp1 has the same coordiates (chr1:10053629-10189988) as the second gene Arfgef1. But in my mouse gtf file (from Ensembl), the coordinates for those two genes are:
Cspp1: Chromosome 1: 10,028,299-10,126,849
Arfgef1: Chromosome 1: 10,127,652-10,222,751
Those two genes are not overlapped. Why do they have the same coordinates in gene_exp.diff file?
Thank you very much!
However, I checked one of the cuffdiff output files: gene_exp.diff. I found there is still multiple FPKM problem for many genes (see below):
XLOC_000009 Cspp1 chr1:10053629-10189988 q1 q2 OK 44.5012 58.359 0.271096 -2.93789 0.00330457 yes
XLOC_000010 Arfgef1 chr1:10053629-10189988 q1 q2 OK 10.0582 7.68137 -0.269589 4.88261 1.04688e-06 yes
XLOC_000011 Arfgef1 chr1:10053629-10189988 q1 q2 OK 40.66 31.8566 -0.244 17.6406 0 yes
XLOC_000013 Arfgef1 chr1:10053629-10189988 q1 q2 OK 2.7768 40.8059 2.68753 -144.972 0 yes
XLOC_000015 Arfgef1 chr1:10053629-10189988 q1 q2 OK 54.0345 65.0081 0.18489 -12.9339 0 yes
XLOC_000016 Arfgef1 chr1:10053629-10189988 q1 q2 OK 23.4654 43.6672 0.62107 -29.4492 0 yes
XLOC_000031 Tram2 chr1:20986216-20997026 q1 q2 OK 5.8219 2.96147 -0.67594 3.70609 0.000210487 yes
XLOC_000032 Tram2 chr1:20986216-20997026 q1 q2 OK 3.33419 14.9065 1.49757 -29.7646 0 yes
XLOC_000057 Tmem131 chr1:36849038-36996484 q1 q2 OK 37.3723 30.8444 -0.191975 5.03247 4.84195e-07 yes
Did I do something wrong? Wht do some genes only have one FPKM (one row) and some genes have multple FPKM (multple rows)?
I have another question regarding gene_exp.diff file. The first gene Cspp1 has the same coordiates (chr1:10053629-10189988) as the second gene Arfgef1. But in my mouse gtf file (from Ensembl), the coordinates for those two genes are:
Cspp1: Chromosome 1: 10,028,299-10,126,849
Arfgef1: Chromosome 1: 10,127,652-10,222,751
Those two genes are not overlapped. Why do they have the same coordinates in gene_exp.diff file?
Thank you very much!
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