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Posts by Ekalavya
... rmsk primary table has > 5 million records for repetitive elements. There were 989434 entries belong to "LINE" class of repeat. When I checked the lengths of these LINEs, a majority of them (973906) were shorter than 5kb. I took the "genoStart" and "genoEnd" to calculate the lengths. Aren't these ...
... A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`). `--fr`/`--rf`/`--ff`: The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. ...
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