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cpouchon / ORTHOSKIM

ORTHOSKIM allows in silico capture of targeted sequences in genomic or transcriptomic libraries.
GNU General Public License v3.0
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Code bug related to capture nuclear DNA sequences #11

Open bheimbu opened 2 years ago

bheimbu commented 2 years ago

Hi @cpouchon,

it's me again. I might have found a bug in your code. When I want to capture nuclear DNA sequences using ./orthoskim -m capture -t nucrdna -c config_orthoskim.txt, ORTHOSKIM ends with an error that the infile ($NRDNA_ANNOTATIONS) is not specified. However, a closer look (see picture) reveals that ORTHOSKIM is looking for the $MITO_ANNOTATIONS, but why? Actually when I define $MITO_ANNOTATIONS the above mentioned command runs but is looking for mitochondrial sequences, while I want nuclear sequences?!

Cheers Bastian

cpouchon commented 2 years ago

Hi Bastian, when you want targeting one of the rDNA, mtDNA (and cpDNA for plants), you have to give all the genomic regions (annotations) as a selection between the two (or three) regions is done. Here, you need to give the $MITO_ANNOTATIONS to target the rDNA sequences also. The first step is to assign your contigs to mtDNA or rDNA this why you have the ExtractGenome function working on the mtDNA.