Commit c739ea3c authored by Mikaël Salson's avatar Mikaël Salson

doc/: Vocabulary uniformization between user.md and tutorial

Segmenter is sequence panel (was sequence view in user.md)
parent 021dba85
......@@ -184,9 +184,9 @@ By default in the bottom plot (the \textit{grid}), the clones
maintaining down the left button of the mouse.}
The sequences of the clones now appear in the bottom part of the browser (the
\textit{segmenter}). If many clones are selected you can view more sequences
by moving the mouse above the segmenter.
The sequences in the segmenter can be visually compared but you can also align
\textit{sequence panel}). If many clones are selected you can view more sequences
by moving the mouse above the sequence panel.
The sequences in the sequence panel can be visually compared but you can also align
them to see more easily their similarities.
\question{\new XXX Pin the segmenter}
......@@ -196,12 +196,12 @@ emphasized in bold.}
Now it is the user's expertise to determine if sequences are sufficiently
similar, depending on her or his specific question. If some sequences don't appear to be similar enough, you can remove
them from the segmenter by clicking on the cross in front of the sequence in
the segmenter.
them from the sequence panel by clicking on the cross in front of the sequence in
the sequence panel.
\question{Remove all the sequences that are not similar enough with the first
one.}
Now all the sequences in the segmenter should be highly similar. All their
Now all the sequences in the sequence panel should be highly similar. All their
differences could be due to sequencing or PCR errors.
These artifacts (mutations, homopolymers, insertions, deletions)
depend on the sequencer and the PCR technique.
......@@ -409,18 +409,18 @@ Another option is to directly plot a log-log curve comparing two samples.
\subsection{Checking VDJ designations with other software}
For some studies, VDJ designations are very important.
In the list and in the segmenter, those designations are written in their
In the list and in the sequence panel, those designations are written in their
short form.
\question{Put the mouse cursor over a clone. In the status bar (between the
grid and the segmenter), the complete designation appears.}
grid and the sequence panel), the complete designation appears.}
We can double check this designation with other popular software.
\question{Select a few clones.}
\marginpar{This requires an internet connection.}
\question{Click on the down triangle, which is right to \com{IMGT/V-QUEST}. The
clone sequences are sent to IMGT/V-QUEST.}
\question{Then tick the checkbox 5'V/D/3'J. In the segmenter the boundaries of
\question{Then tick the checkbox 5'V/D/3'J. In the sequence panel the boundaries of
the V(D)J genes as computed by IMGT/V-QUEST are underlined.}
Note that data returned by IMGT/V-QUEST is available by clicking on the \textit{i} icon of analyzed clones,
......
......@@ -187,9 +187,9 @@ or their “N length” (that is N1-D-N2 in the case of VDJ recombinations).
- The “★” button (status bar, bottom right) allows
to tag at once all the selected clones.
## The sequence view (bottom panel)
## The sequence panel (bottom panel)
The sequence view displays nucleotide sequences from selected clones.
The sequence panel displays nucleotide sequences from selected clones.
- See "[What is the sequence displayed for each clone ?](#what-is-the-sequence-displayed-for-each-clone)" below
- Sequences can be aligned together (“align” button), identifying substitutions, insertions and deletions. Silent mutations are identified, as soon as a CDR3 is detected, and represented with a double border in blue.
......@@ -374,7 +374,7 @@ Note that the algorithm also detects some VDDJ or VDDDJ recombinations that may
Some incomplete or unusual rearrangements (Dh/Jh, Dd2/Dd3, KDE-Intron, mixed TRA-TRD recombinations) are also detected.
Once clones are selected, you can send their sequence to **IMGT/V-QUEST** and **IgBlast**
by clicking on the links just above the sequence view (bottom left).
by clicking on the links just above the sequence panel (bottom left).
This opens another window/tab.
# Can I see all the clones and all the reads ?
......
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