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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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second pass STAR #22

Closed lindongdo closed 5 years ago

lindongdo commented 5 years ago

Hi, I am running JUM the latest version 2.0.2 by following the manual https://github.com/qqwang-berkeley/JUM/wiki/3.1.-Manual-running-JUM-(v2.0.2-and-up), which looks different to previous 2.0 version especially in inputs. There are two passes of STAR mapping in previous version but I couldn't find it in the latest version manual. Do we still need to follow previous pipeline to run two passes of STAR as the input in the latest version?

Thanks

Dong

qqwang-berkeley commented 5 years ago

Hi,

I changed the two passes of STAR for input from v2.0 to just one round in v2.0.2 because STAR now integrates two passes of mapping into one round during a recent upgrade . You can simply follow the instructions in the latest version. It is just easier - one step less.

Best,

Qingqing

On Fri, Jul 26, 2019 at 8:42 AM Dongdong Lin notifications@github.com wrote:

Hi, I am running JUM the latest version 2.0.2 by following the manual https://github.com/qqwang-berkeley/JUM/wiki/3.1.-Manual-running-JUM-(v2.0.2-and-up), which looks different to previous 2.0 version especially in inputs. There are two passes of STAR mapping in previous version but I couldn't find it in the latest version manual. Do we still need to follow previous pipeline to run two passes of STAR as the input in the latest version?

Thanks

Dong

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