HiTC problem exporting to my5C

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sergio.espeso-gil • 0

@sergioespeso-gil-6997

Last seen 4.9 years ago

New York

Hi community!

I am not sure if I miss a dependency, but when I am trying to export HiC data mapped to hg38 to a my5C file, even though I add << genome="hg38" >> the headers say: 1|mm9|chr1:1-100000

Is this a bug? Or I am missing a dependency?

x<-importC("hESC100000.matrix", xgi.bed="hESC100000_abs.bed") show(x) export.my5C(x, file="hESC.export5C", genome="hg38", per.chromosome=FALSE)

Thanks!!!!

S.

HiTC HiC-Pro • 1.2k views

ADD COMMENT • link 4.9 years ago sergio.espeso-gil • 0

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Hi, Could you please specify which HiTC version you are using ? Thanks. Nicolas

ADD REPLY • link 4.9 years ago Nicolas Servant ▴ 260

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Hi Nicolas,

I am using R version 3.5.1 and HiTC version '1.26.0'

Should I upgrade to version 1.30?

Much appreciated

ADD REPLY • link 4.9 years ago sergio.espeso-gil • 0

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Indeed, I think there is a small bug if the input object is an HTClist ... sorry for that. To move forward, a simple sed on the my5C file should allow you to change all mm9, to hg18. I will try to fix this as soon as possible. Best

ADD REPLY • link 4.9 years ago Nicolas Servant ▴ 260

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No problem, all good.

Thanks a lot Nicolas!

ADD REPLY • link 4.9 years ago sergio.espeso-gil • 0

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Entering edit mode

Indeed, I think there is a small bug if the input object is an HTClist ... sorry for that. To move forward, a simple sed on the my5C file should allow you to change all mm9, to hg18. I will try to fix this as soon as possible. Best

ADD REPLY • link 4.9 years ago Nicolas Servant ▴ 260

0

Entering edit mode

Indeed, I think there is a small bug if the input object is an HTClist ... sorry for that. To move forward, a simple sed on the my5C file should allow you to change all mm9, to hg18. I will try to fix this as soon as possible. Best

ADD REPLY • link 4.9 years ago Nicolas Servant ▴ 260

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