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cmayer / MitoGeneExtractor

The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.
GNU Affero General Public License v3.0
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Dealing with introns #12

Open riksub opened 1 month ago

riksub commented 1 month ago

Hi,

I was trying to test the software to extract nuclear coding genes with introns, but apparently, it retrieves only the first open reading frame and misses the rest of the coding gene. Is there any option to deal with that or is it just out of the target of the software?

R.

marievalerie commented 1 month ago

Hi, how can you extract the first open reading frame? Or do you mean the first exon of your nuclear gene?

Extracting nuclear genes which have introns is not the target of the software. It might work if you have RNA-seq data (no introns in the reads) and the correctly spliced protein reference, but we never tested it.

best wishes, marie