Lastz align sequence to self in blocks of 1kb
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Entering edit mode
7 weeks ago
polag01 ▴ 10

Hi all,

Sorry if this has been asked before, but I seem not to have found the answer.

I want to do a self-alignment of a 60Mb chromosome using a window size of 1kb.

First, the --self option does not run, so I opt for specifying the same sequence as the query and as the target, so I ended up with the command as follows:

lastz $inFile1[unmask] $inFile1[unmask] \ --notransition --step=20 --nogapped \ --format=general > $outFilePath"/"$sample"_identity_general.txt" The command ran correctly and I ended up with about 81GB size file as output.

Second, is the "--step" option specifying the window size (documentation mentioned seed length, is it the same as window size), and if not, how do I specify a 1kb window size for the alignment (I seem not to be able to locate this on the documentation page).

Thank you.

LASTZ chromosome self-align • 156 views
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