Commit 9c8e4913 authored by Mikaël Salson's avatar Mikaël Salson
Browse files How to visualize clone coverage

parent 08cd4e1e
......@@ -302,11 +302,16 @@ There can be several causes leading to bad ratios:
between .85 and 1 is quite frequent. On the contrary, if it is .5 it means that the consensus sequence
length is half shorter than the median read length in the clone.
There is a bad clone coverage ($<.5$) when reads do share the same window
There is a bad clone coverage (< 0.5) when reads do share the same window
(it is how Vidjil defines a clone) and when they have frequent discrepancies
outside of the window. Such cases have been observed with chimeric reads
which share the same V(D)J recombinations in their first half and have
totally different and unknown sequences in their second half.
In the browser, the clones with a low clone coverage (< 0.5) are displayed in
the list with an orange I on the right. You can also visualize the clones
according to their clone coverage by selecting for example “clone
coverage/GC content” in the preset menu of the “plot” box.
* Keyboard shortcuts
** Browser
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