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Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case #1879

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nathandunn opened this issue Apr 20, 2018 · 1 comment
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Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case #1879

nathandunn opened this issue Apr 20, 2018 · 1 comment
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2.1.0

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nathandunn commented Apr 20, 2018 •
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From:

http://gmod.827538.n3.nabble.com/splice-sites-aren-t-recognized-when-genomic-fasta-is-lowercase-td4059348.html

Sometimes, the genomic fasta will contain lower-case sequence (usually when it's soft-masked). Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case. In the following 2 examples, the model is on the + strand
@nathandunn nathandunn added this to the 2.0.9 milestone Apr 20, 2018
@nathandunn nathandunn self-assigned this Apr 20, 2018
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splice_1
splice2

This was referenced Apr 20, 2018
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@ghost ghost assigned deepakunni3 Apr 21, 2018
@ghost ghost added the in progress label Apr 21, 2018
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@nathandunn nathandunn modified the milestones: 2.0.9, 2.1.0 Jun 12, 2018
@nathandunn nathandunn mentioned this issue Oct 4, 2018
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