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vidjil
vidjil
Commits
20e443ff
Commit
20e443ff
authored
Nov 26, 2014
by
Mathieu Giraud
Browse files
algo.org: VJ/VDJ instead of TRG/IGH
parent
440b5a25
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1
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doc/algo.org
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20e443ff
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@@ -155,8 +155,8 @@ explanation can be found in the paper. More help on that will be
available in the following months. The defaults values should work.
The =-w= option fixes the size of the "window" that is the main
identifier to gather clones. The defaults values (40 for
TRG
, 60 for
IGH
) were selected to ensure a high-quality clone gathering. The
identifier to gather clones. The defaults values (40 for
VJ
, 60 for
VDJ recombinations
) were selected to ensure a high-quality clone gathering. The
high-throughput heuristic predicts the center of the "window" that may
be shifted by a few bases from the actual "center" of the CDR3 (for TRG,
less than 15 bases compared to the IMGT/V-QUEST or IgBlast prediction
...
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@@ -164,7 +164,7 @@ in >99% of cases). The extracted window should be large enough to
fully contain the CDR3 as well as some part of the end of the V and
the start of the J to uniquely identify a clone.
Setting =-w= to 30 for
TRG
and 50 for
IGH
may "segment" (analyze) a
Setting =-w= to 30 for
VJ
and 50 for
VDJ recombinations
may "segment" (analyze) a
few more reads, but may in some rare cases falsely cluster reads from
different clones. Setting =-w= to lower values is not recommended.
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