Commit 20e443ff authored by Mathieu Giraud's avatar Mathieu Giraud
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algo.org: VJ/VDJ instead of TRG/IGH

parent 440b5a25
......@@ -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
......@@ -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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