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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Unrecognized option --variable-read-lengths #96

Closed dputhier closed 12 years ago

dputhier commented 12 years ago

Dear all, I'm running the following command:

rum_runner align -i /RUMIndex/indexes/mm9 -o RUM --chunks 8 --platform Local --name myRNA_PolyA --limit-bowtie-nu --limit-nu 60 --variable-read-lengths merge.fastq

Output is

Usage errors:

Unrecognized option --variable-read-lengths

Usage: rum_runner align [OPTIONS] [FORWARD [REVERSE]]

Any Idea ?

mdelaurentis commented 12 years ago

It looks like that's a discrepancy between the documentation and the actual options it's looking for. The option that the program looks for is "--variable-length-reads", not "--variables-read-lengths". Can you please try it with "--variable-length-reads" instead? I'll change the documentation. Thanks for pointing this out!

dputhier commented 12 years ago

That's it. Thanks for quick reply

2012/8/2 Mike DeLaurentis < reply@reply.github.com

It looks like that's a discrepancy between the documentation and the actual options it's looking for. The option that the program looks for is "--variable-length-reads", not "--variables-read-lengths". Can you please try it with "--variable-length-reads" instead? I'll change the documentation. Thanks for pointing this out!

Reply to this email directly or view it on GitHub: https://github.com/PGFI/rum/issues/96#issuecomment-7455095

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