What's the difference between lower cases and the upper cases in splice_site in janno file?

ylab-hi / ScanExitron

A computational workflow for exitron splicing identification

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What's the difference between lower cases and the upper cases in splice_site in janno file? #3

Closed ptnaimelmm closed 3 years ago

ptnaimelmm commented 3 years ago

Hi, What's the difference between lower cases and the upper cases in splice_site column in janno file? Take GT-AG as an example, gt-ag gt-aG gt-Ag gt-AG gT-ag gT-AG Gt-ag Gt-aG Gt-AG GT-ag GT-aG GT-Ag GT-AG

Thanks

dolittle007 commented 3 years ago

RegTools extract these splice sites from the human reference genome FASTA file directly. Here shows the answers. https://bioinformatics.stackexchange.com/questions/225/uppercase-vs-lowercase-letters-in-reference-genome