Commit 80ff1083 authored by Mathieu Giraud's avatar Mathieu Giraud

algo.org: update documentation

parent cd2187a3
......@@ -430,9 +430,9 @@ The following unsegmentation causes are reported:
|---------------------+---------------------------------------------------------------------------------------------------------------------|
| =UNSEG too few V/J= | No information has been found on the read: There are not enough similarities neither with a V gene or a J gene. |
|---------------------+---------------------------------------------------------------------------------------------------------------------|
| =UNSEG only V= | Relevant similarities have been found with some V, but not enough with any J. |
| =UNSEG only V/5= | Relevant similarities have been found with some V, but not enough with any J. |
|---------------------+---------------------------------------------------------------------------------------------------------------------|
| =UNSEG only J= | Relevant similarities have been found with some J, but not enough with any V. |
| =UNSEG only J/3= | Relevant similarities have been found with some J, but not enough with any V. |
|---------------------+---------------------------------------------------------------------------------------------------------------------|
| =UNSEG ambiguous= | Vidjil finds some V and J similarities mixed together which makes the situation ambiguous and hardly solvable. |
|---------------------+---------------------------------------------------------------------------------------------------------------------|
......@@ -446,7 +446,7 @@ Some datasets may give reads with many low =UNSEG too few= reads:
- =UNSEG too few V/J= usually happens when reads share almost nothing with the V(D)J region.
This is expected when the PCR or capture-based approach included other regions, such as in whole RNA-seq.
- =UNSEG only V= and =UNSEG only J= happens when reads do not span enough the junction zone.
- =UNSEG only V/5= and =UNSEG only J/3= happen when reads do not span enough the junction zone.
Vidjil detects a “window” including the CDR3. By default this window is 50bp long,
so the read needs be that long centered on the junction.
......
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