rpkm and raw count

Question

[bahare.a.1370]

How can I convert rpkm to raw count? Can I compare RNA-seq data of two different cell line with different platform (hiseq2000 and ion torrent)?

Answer 1

[Hussain Ather]

Multiple RPKM by exon length and by number of reads mapped in the sample, then divide by 1,000,000 to get raw count.

Or you could use bedtools coverageBed with the tophat bam file and with a bed file of the genes.

[lshepard]

To add to the answer, you can compare sequencing data across the platforms as long as you know what is expected to potentially differ (although as the literature shows, there is good concordance between them). As to the cell lines, that depends upon what kind of questions you are trying to answer, but if you have say a cell line A in Illumina and cell line B in Torrent, I would say that this might be a bit tricky as some differences may be dependent upon platform and other sequencing factors (read depth, length etc...). That is not to say that you can't do it...

Personally, I would feel more comfortable (and have done this in the past), to use both technologies under the same experimental conditions.