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smangul1 / rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
https://github.com/smangul1/rop/wiki
GNU General Public License v3.0
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New bug in rop-imrep.sh ... #121

Closed PoslavskySV closed 7 years ago

PoslavskySV commented 7 years ago

When running:

./rop-imrep.sh some.bam some.output ""

the following error occurs:

./rop-imrep.sh: line 4: ./argparse.bash: No such file or directory
./rop-imrep.sh: line 5: argparse: command not found

I suppose lines 4-5 in rop-imrep.sh are incorrect.

smangul1 commented 7 years ago

Hi, Sorry for the delay with the answer. Please use imrep tool . Now it supports bam files with a mixture of mapped and unmapped reads. Please just use github clone to get a new version and read manual here : https://github.com/mandricigor/imrep/wiki/Run-ImReP-for-bams-(with--mapped-and-unmapped-reads)

smangul1 commented 7 years ago

Let me know if you have any other questions. Otherwise i will close the issue