One of the easy way to achieve read count and RPKM file

Tutorial:One of the easy way to achieve read count and RPKM file

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7.3 years ago

maleknias ▴ 40

You can go to web: https://jhubiostatistics.shinyapps.io/recount/
Type your study ID in search box, like; SRP066834.
Based on any biological requirement like gene, exon, junction or phenotype, you can download read count table, RSE (RData file) and link to other information.
If you want RPKM of gene, you can get it by "recount" package in R.

R code:

library('recount')
rse <- scale_counts(rse_gene)
RPKM=getRPKM(rse)
write.csv(RPKM, file = RPKM.csv')

Attention: Your study may NOT be available on this site.

RNA-Seq • 2.0k views

ADD COMMENT • link updated 18 months ago by Ram 44k • written 7.3 years ago by maleknias ▴ 40

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Thanks for sharing!

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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