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BUStools / bustools

Tools for working with BUS files
https://bustools.github.io/
BSD 2-Clause "Simplified" License
92 stars 23 forks source link

problem with bustools capture #13

Closed raymondlouie closed 5 years ago

raymondlouie commented 5 years ago

In the tutorial

https://www.kallistobus.tools/velocity_tutorial.html

it says to run

bustools capture -o introns_capture/ -c ../introns_transcripts.to_capture.txt -e matrix.ec -t transcripts.txt output.correct.sort.bus

However, I get the error message:

Error: capture list type must be specified (one of -s, -u, or -b)

If I then run with the -s command:

bustools capture -s -o introns_capture/ -c ../introns_transcripts.to_capture.txt -e matrix.ec -t transcripts.txt output.correct.sort.bus

there is nothing outputted in the introns_capture folder?

A related question: when I type "bustools capture", it says the output should be a file, not a directory:

Usage: bustools capture [options] bus-files

Options: -o, --output File for captured output

but the help-page

https://github.com/BUStools/bustools

says the output should be a directory:

Usage: bustools capture [options] bus-files

Options: -o, --output Directory for output

Thanks.

sbooeshaghi commented 5 years ago

The recent merge of the pull request to master means that those cloning the repo and compiling from source have a different version of capture than in the binary.

We will update the tutorial accordingly. In the meantime, the tutorial will work with the bustools binary v0.39.2 available here https://bustools.github.io/download

raymondlouie commented 5 years ago

Great thanks, it's working now.