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Old 03-04-2012, 04:32 PM   #1
fgh1124
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Default Help! How to calculate gene expression level (RPKM) in RNA-seq experiment

HI, everyone!

I just want to know each gene's expression level not the transcript isoforms. I have alignment data formated in SAM/BAM and annotation file in gtf/gff/bed. Some genes position have overlap with other genes. So I want to know which software is suitable for my question except for cuffdiff or cufflinks?

Thanks for your time!
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Old 03-05-2012, 04:01 AM   #2
pbluescript
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You could try RSEM:

http://deweylab.biostat.wisc.edu/rsem/
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Old 07-31-2014, 06:09 AM   #3
Mike2188
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Both cufflinks and cuffdiff will generate FPKM data. Cuffdiff will also spit out differentially expressed genes between your samples and take a bit longer.
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