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In minimap the -G parameter decides the maximum gap on the reference during spliced alignments. So I take this as either intron length or intergenic length. Is my assumption correct? This is set to 200000 by default. I set the -G value to 50000 for my species, as the 90th percentile value of intron length was 48000. It turns out that the gene I was interested in had a single 60000 bp intron. Therefore, FLNC reads that should have aligned did not, as I set -G 50000. When I ran minimap with default -G the reads aligned fine. Therefore, a few questions.
Is it advisable to reduce this size closer to the anticipated intron size of a species?
How strictly does the tool adhere to the -G parameter value? You mention that this has an effect on the chaining and alignment band width. Which are these parameters? and what do they control?
Thanks
Abhijit
The text was updated successfully, but these errors were encountered:
Hello,
In minimap the
-G
parameter decides the maximum gap on the reference during spliced alignments. So I take this as either intron length or intergenic length. Is my assumption correct? This is set to 200000 by default. I set the-G
value to 50000 for my species, as the 90th percentile value of intron length was 48000. It turns out that the gene I was interested in had a single 60000 bp intron. Therefore, FLNC reads that should have aligned did not, as I set-G 50000
. When I ran minimap with default-G
the reads aligned fine. Therefore, a few questions.-G
parameter value? You mention that this has an effect on the chaining and alignment band width. Which are these parameters? and what do they control?Thanks
Abhijit
The text was updated successfully, but these errors were encountered: