The result in my genes_fpkm.tracking file is like
XLOC_000011 XLOC_000011 LOC_Os01g01140 TSS15 Chr1:69674-70131 0 0 0 0 0 0 0
XLOC_000012 XLOC_000012 LOC_Os01g01150 TSS16 Chr1:72774-80256 16.31 12.84 13.42 17.44 14.96 14.89 14.59
XLOC_000013 XLOC_000013 LOC_Os01g01160 TSS17 Chr1:82427-84302 15.5 6.2 12.92 23.95 13.51 20.14 10.82
XLOC_000014 XLOC_000014 LOC_Os01g01170 TSS18 Chr1:85336-88844 1.33 0.32 0.73 1.17 0.67 1.3 0.26
XLOC_000015 XLOC_000015 LOC_Os01g01200 TSS19 Chr1:95498-98558 0 0 0 0 0 0 0
Also from my gene_exp.diff
XLOC_000011 XLOC_000011 LOC_Os01g01140 Chr1:69674-70131 IR64_CT IR64_DS 0 0 -13.54 0 1
XLOC_000012 XLOC_000012 LOC_Os01g01150 Chr1:72774-80256 IR64_CT IR64_DS 16.31 12.84 -13.21 -0.44 0.66
XLOC_000013 XLOC_000013 LOC_Os01g01160 Chr1:82427-84302 IR64_CT IR64_DS 15.5 6.2 -12.68 -1.82 0.24
XLOC_000014 XLOC_000014 LOC_Os01g01170 Chr1:85336-88844 IR64_CT IR64_DS 1.33 0.32 -12.6 -1.39 0.19
XLOC_000015 XLOC_000015 LOC_Os01g01200 Chr1:95498-98558 IR64_CT IR64_DS 0 0 -12.56 0 1
I want to find differentially expressed genes. Can I do it from 1st file or I have to go for gene_exp.diff? Also how can a heatmap be generated?
I did make a fpkm matrix out of genes.fpkm_tracking and do I have to take fpkm>=0/1 in any tissue? Also how to calculate up regulated and down regulated?
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written
by
dineshtripathy9658 •
3 answers
May be you should read the documentation once cuffdiff-output-files
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written
by
GouthamAtla
As @Geek_y says, you can use cuffdiff output file like for DE genes,
For heatmap you can use Pheatmap package in R which helps you to create lots of heatmap so easily.
For up and down regulated genes please see this page: Understanding up and down regulated genes from LOG2 foldchange or foldchange
This workflow can come useful to you!
http://www.bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf
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Hello everyone
I am using cufdiff . I followed steps tophat, -> cufflink->cuffmerge->cuffdiff . I have three query's...
Firstly, I used the gff file in tophat, cufflink and cuffmerge step. For my species, gtf is not available. I want to know using gff instead of gtf will make any difference in result or not?
Secondly I am not getting geneid name in cuffdiff output files.
At last , I lost some of the coordinate in cuffdiff result, initially I had 76000 genes coordinate in my gff file, but I am getting fpkm of 75000 coordinate only in
genes.fpkm.trackingPlease reply as soon as possible
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