Converting amplicon coordinates to genomic

Converting only ~/test

~/auxiliary_tools/convert2genomic.pl -t ~/test/target_specification.txt -d ~/test/directories/strict/ -p 1000 > test.bed

Converting all finished regions

~/auxiliary_tools/convert2genomic.pl -t ~/design/target_specification.txt -d ~/design/directories/strict/ -p 1010 > amplicons.bed

Obtaining uncovered regions

grep Uncovered amplicons.bed > uncovered.bed

Rose, notice that the offset was 1010, not 950. I don’t understand why, but that’s what I get when I BLAT a primer then check the coordinates. See if you figure out why this is happening.

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