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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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[bug] target_mapping hangs #121

Open pmelsted opened 7 years ago

pmelsted commented 7 years ago

(originally filed in kallisto repo by @egenomics)

If the target_mapping file contains more than two columns sleuth hangs in the reading counts step.

pmelsted commented 7 years ago

Don't know if this was fixed in v0.29

warrenmcg commented 7 years ago

Hi @pmelsted, what version were you using? And what does the troublemaker file look like? My target_mapping data frame has always had more than two columns and I've never experienced this issue using sleuth.

pimentel commented 7 years ago

Here is the original bug report: https://github.com/pachterlab/kallisto/issues/136

@egenomics could you please provide the specifics that @warrenmcg requested above?

thank you,

harold

egenomics commented 7 years ago

Package sleuth version 0.28.1 The file is tab separated, containing n columns.

warrenmcg commented 7 years ago

Thanks for responding! If it's small enough when compressed, could you send it? If it's too big, could you send a subset that still reproduces the problem?

I would like to see if I can reproduce the problematic behavior on my end. As I said, I have never experienced an issue using more than two columns; however, I have only occasionally read the target mapping from a file. I most often download the annotations using biomaRt.

pimentel commented 7 years ago

ping @egenomics

thanks