Transfer CDS for alternative GTF transcripts and exons without strand annotations

smith-chem-wisc / Proteogenomics

C# implementation of classes and functions for proteogenomics

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Transfer CDS for alternative GTF transcripts and exons without strand annotations #7

Open acesnik opened 6 years ago

acesnik commented 6 years ago

Currently, I filter out transcripts lacking strand. In these cases, we could use information from the gene model to look for the best match, use that strandedness if it exists, and filter the strandless transcript if not.

acesnik commented 6 years ago

See https://github.com/smith-chem-wisc/Proteogenomics/blob/master/Proteogenomics/Intervals/Transcript.cs#L889