Commit 49657256 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: documents '-w all'

See #1642.
parent 81ac715d
......@@ -273,7 +273,7 @@ Window prediction
(default: #####-#####, ######-######, #######-#######, depends on germline)
-k <int> k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)
(using -k option is equivalent to set with -s a contiguous seed with only '#' characters)
-w <int> w-mer size used for the length of the extracted window (default: 50)
-w <int> w-mer size used for the length of the extracted window (default: 50) ('all': use all the read, no window clustering)
-e <float> maximal e-value for determining if a segmentation can be trusted (default: 'all', no limit)
-t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: 0) (0: no trim)
#+END_EXAMPLE
......@@ -301,6 +301,10 @@ large D, short or no N regions and almost no somatic hypermutations). However, s
may "segment" (analyze) less reads, depending on the read length of your data, and may also
return more clones, as any sequencing error in the window is not corrected.
The special =-w all= option takes all the read as the windows, completely disabling
the clustering by windows and generally returning more clones. This should only be used on
datasets where reads of the same clone do have exactly the same length.
Setting =-w= to lower values than 50 may "segment" (analyze) a few more reads, depending
on the read length of your data, but may in some cases falsely cluster reads from
different clones.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment