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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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Problems with runall_sam2mappingstats.pl #26

Closed jenruss closed 10 years ago

jenruss commented 10 years ago

I found two problems with the scripts runall_sam2mappingstats.pl. First of all, the script started running but never finished. I checked the script and I found a typo in line 156. There you have '$sample_dir' instead of '$sampledirs' specified earlier. Secondly, currently if you do not have the file with the total reads, the script only works if you have used the 'merged' option. But I only wanted to look at unique reads. I changed the script for my purposes, but maybe this should be added as an option to the script.

Thanks, Jenny

eunjijunekim commented 10 years ago

Thanks for catching the typo and reporting the issue. I've added -norm_u and -norm_nu options to runall_sam2mappingstats.pl and getstats.pl script, so you can use them for the unique reads. Eun Ji