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added new scripts to BuildIndices docker for marmoset #155

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merged 4 commits into from
Jan 17, 2025
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ekiernan
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@ekiernan ekiernan commented Jan 16, 2025

This PR adds new scripts to the BuildIndices docker to handle processing the marmoset GTF used for the BICAN.

Specifically, it includes a script create_marmoset_header.py that adds a new header to the marmoset GTF file and puts mitochondrial genes at the bottom of the GTF with a new "gene" tag in the 3rd field.

The second script is a create_gtf_marmoset.py that takes the output of the create_marmoset_header.py and modifies the GTF to be compatible with indexing for STARsolo alignment.

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@nikellepetrillo nikellepetrillo left a comment

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this looks good to me, liz! thank you

@ekiernan ekiernan merged commit 9b82dec into develop Jan 17, 2025
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@aawdeh aawdeh left a comment

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LGTM!

@ekiernan
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These scripts are captured in BuildIndices docker version 2.1.0

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3 participants