Hi ! I have a table (58037×117) contain scaled read count for 117 sample (case and control) and gff and gtf file. Considering of RPKM calculation: RPKM=(row number of reads/exon length) ×(1000 000 / number of mapped reads in the sample) how can I get a table (58037×117) contain RPKM?? Is it solution based of use galaxy?
•
written
by
maleknias •
In the original publication by Ali Mortazavi et al. they provide the means to do so: http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1226.html?foxtrotcallback=true
If you are searching for a more "divulgative" article on the topic, this is the most linked one: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
Finally, a remark: I would suggest you to switch to TPM. Mortazavi himself suggested not to use RPKM anymore.
Thanks but it's not useful for me. I want to save time and because sample size is big i want use table of read-count. so do it again from the beginning is not cost effective!!
You don't need to do everything from the beginning, it just takes some command line used differently because the formula is different.
1) Enter "#" for your matrix header
2) Add one extra column to your matrix in the end (exon/gene length)
3) Use the following script according to the instructions,
thanks a lot. It seems cool. could you guide me "how I can make .count file" ?? Is this make by "Count.seqs" and "mothur_toolsuit" ?
count file can be any matrix of raw count (Gene id in the first column+followed by counts+followed by Gene/exon length) created by read quantification programs like 'featureCounts' and 'HTSeq'. For getting sum of exon length gene-wise 'featureCounts' is well suited program.
Log in to answer this question.
