Tutorial:One of the easy way to achieve read count and RPKM file
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6.8 years ago
maleknias ▴ 40
  1. You can go to web: https://jhubiostatistics.shinyapps.io/recount/
  2. Type your study ID in search box, like; SRP066834.
  3. 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.
  4. 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 • 1.9k views
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Thanks for sharing!

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