Commit befff7cc authored by Mikael Salson's avatar Mikael Salson

algo.org: Few typos

parent ba379f1a
......@@ -98,7 +98,7 @@ 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
high-throughput heuristic predicts the center of the "window" that may
shifted by a few bases from the actual "center" of the CDR3 (for TRG,
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
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
......@@ -139,14 +139,14 @@ The =-z= option limits the number of clones that are fully analyzed,
/with their V(D)J segmentation/, in particular to enable the browser
to display the clones on the grid (otherwise they are displayed on the
'?/?' axis).
If you want have to analyze more clones, you should use =-z 50= or
=-z 100=. It is not recommended to use larger values: outputing more
than 100 clones is often not useful to visualize browser
visualization, and takes large computation time.
If you want to analyze more clones, you should use =-z 50= or
=-z 100=. It is not recommended to use larger values: outputting more
than 100 clones is often not useful since they can't be visualized easily
in the browser, and takes large computation time.
Note that even if a clone is not in the top 20 (or 50, or 100) but
still passes the =-R=, =-%= options, it is still reported in the .data
file. If the clone is at some MRD point in the top 20 (or 50, or 100),
it will be fully analyzed/segmented by this other point (and the
it will be fully analyzed/segmented by this other point (and then
collected by the =fuse.py= script, and then, on the browser, correctly
displayed on the grid).
......
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