error in tximport command
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2.4 years ago
StartR ▴ 20

when I am typing command : txi <- tximport(samples, type = "stringtie", tx2gene = tx2gene)

I am getting this error:

Error in match.arg(type, c("none", "kallisto", "salmon", "sailfish", "rsem")) : 
  'arg' should be one of “none”, “kallisto”, “salmon”, “sailfish”, “rsem”

I am using t_data.ctab files from STRINGTIE output.

Please help

tximport • 546 views
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Entering edit mode
2.4 years ago
ATpoint 65k

You are probably using an old version that did not yet support stringtie import. I suggest you update tximport and try again. stringtie support was added with version 1.8.0, see https://bioconductor.org/packages/release/bioc/news/tximport/NEWS

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Yes, you were right, thank you!

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