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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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Implement a secondary mapper with lower memory footprint #90

Closed frenkiboy closed 3 years ago

frenkiboy commented 3 years ago

A mapper with lower memory footprint might be useful for cloud operations - Hisat2: http://daehwankimlab.github.io/hisat2/

rekado commented 3 years ago

See https://github.com/BIMSBbioinfo/pigx_rnaseq/pull/93

This replaces STAR with Hisat2. Would you prefer to give users the choice?

al2na commented 3 years ago

I think yes, if possible. STAR is the standard currently

On Thu, Mar 11, 2021 at 5:37 PM rekado @.***> wrote:

See #93 https://github.com/BIMSBbioinfo/pigx_rnaseq/pull/93

This replaces STAR with Hisat2. Would you prefer to give users the choice?

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rekado commented 3 years ago

It's possible. We just need to decide if this should be a runtime selection or a configure-time selection. Configure-time means that we can build a variant of pigx-rnaseq that only supports STAR, or a variant that supports Hisat2. Runtime means that both aligners must be installed, but it's more flexible for users.

borauyar commented 3 years ago

94