error in tximport command

Question

[StartR]

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

Answer 1

[ATpoint]

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

[StartR]

Yes, you were right, thank you!