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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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splicing mapping mode for RNA-seq is supported? #35

Closed y9c closed 2 months ago

y9c commented 2 months ago

The document does not show an argument for splicing mapping for RNA-seq data, but the code shows RNA-seq filtering step. I wonder if this tool is comparable with RNA-seq data?

Thank you.

https://github.com/smarco/gem3-mapper/blob/82cfcaa0b5ab0c09a94d48375b25883b9d31caf2/resources/gem-tools/tools/gt.filter.c#L63C3-L67

smarco commented 2 months ago

The library has some functions to process SAM files produced by RNA mappers. One of the gem-tools goals was to facilitate the post-processing of SAM/MAP files. However, gem-tools is a different component than the mapper itself gem-mapper.

Let me know if this answers your question.

y9c commented 2 months ago

Thank you for the information.