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thelovelab / tximport

Transcript quantification import for modular pipelines
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Importing transcript abundance datasets generated with Salmon 0.14.0 #29

Closed edoardobertolini closed 5 years ago

edoardobertolini commented 5 years ago

Hi! I have recently updated Salmon to the latest version (0.14.0) and I'm not anymore able to import Salmon outputs into R using the code tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no")

This is the error that I get when I run the code above:

txi <- tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no") reading in files with read_tsv Error in readBin(bootCon, "integer", n = expected.n) : invalid 'n' argument

Any suggestion? Thanks

Edo

mikelove commented 5 years ago

Would you mind posting to Bioc support site and include sessionInfo(). I mainly use GitHub for feature requests but like to have bugs etc reported at Bioc. Did you include bootstraps or Gibbs samples this time? Previously?

mikelove commented 5 years ago

Looks like Rory has a fix, I’ll pull that in a minute, and then I’ll provide code to test the fix on your end

edoardobertolini commented 5 years ago

Thanks! I've included bootstraps when I run Salmon. I will post this to Bioc support. Edoardo

Il giorno lun 10 giu 2019 alle ore 13:05 Mike Love notifications@github.com ha scritto:

Would you mind posting to Bioc support site and include sessionInfo(). I mainly use GitHub for feature requests but like to have bugs etc reported at Bioc. Did you include bootstraps or Gibbs samples this time? Previously?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mikelove/tximport/issues/29?email_source=notifications&email_token=AESVLSRXHFGFAUJO2HTGFYLPZ2JXZA5CNFSM4HWVWBN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXKVGYY#issuecomment-500519779, or mute the thread https://github.com/notifications/unsubscribe-auth/AESVLSUPMOH6EVIPWTDKAR3PZ2JXZANCNFSM4HWVWBNQ .

mikelove commented 5 years ago

Here's how you can test the new fixed version, which Rory just contributed.

library(devtools)
install_github("mikelove/tximport")

Let me know if this fixes it. Thanks!

edoardobertolini commented 5 years ago

It works! Thanks