Commit b5a78e0e authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/user.org: gather some algorithm-dependant aspects into one section

See #2200.
parent 4f299bff
......@@ -261,15 +261,21 @@ The different permissions that can be attributed are:
- View Details: Permissions to view patient/run data in an unencrypted manner for the patients/runs of a group
- Save: Permissions to save an analysis for the patients/runs of a group
* How do you define a clone? How are gathered clones?
Each software has its own definition of what a clone is (or, more precisely
a clonotype). Knowing how clones are defined is important to be aware of the
* How do you define clones, their sequences, and their V(D)J designation?
The Vidjil web application allows to run several RepSeq algorithms.
Each RepSeq algorithm (selected by « config », see above)
has its own definition of what a clone is (or, more precisely
a clonotype), how to output its sequence and how to assign a V(D)J designation.
Knowing how clones are defined is important to be aware of the
potential biases that could affect your analysis.
In Vidjil sequences are gathered into a same clone as long as they share the
** How do you define a clone? How are gathered clones?
In the *built-in Vidjil algorithm*,
sequences are gathered into a same clone as long as they share the
same 50bp DNA sequence around the CDR3 sequence.
In a first step, Vidjil has a quick heuristic which detects approximatively
In a first step, the algorithm has a quick heuristic which detects approximatively
where the CDR3 lies and extracts a 50bp nucleotide sequence centered on that
region. This region is called a window in Vidjil's algorithm. When two
sequences share the same window, they belong to the same clone. Therefore
......@@ -280,9 +286,26 @@ The different permissions that can be attributed are:
inside the cells. Therefore we let the user choose whether the clones should
be manually merged or not.
In MiXCR clones are defined based on the amino-acid CDR3 sequence, on the V
In *MiXCR*, clones are defined based on the amino-acid CDR3 sequence, on the V
gene used and on the hypermutations.
** What is the sequence displayed for each clone ?
<<representative>>
The sequences displayed for each clone are not individual reads.
The clones may gather thousands of reads, and all these reads can have
some differences. Depending on the sequencing technology, the reads
inside a clone can have different lengths or can be shifted,
especially in the case of overlapping paired-end sequencing. There can be also
some sequencing errors.
The =.vidjil= file has to give one consensus sequence per clone, and
Rep-Seq algorithms have to deal with great care to these difference in
order not to gather reads from different clones.
For the *built-in Vidjil algorithm*, it is required that the window centered on
the CDR3 is /exactly/ shared by all the reads. The other positions in
the consensus sequence are guaranteed to be present in /at least half/
of the reads. The consensus sequence can thus be shorter than some reads.
......@@ -333,22 +356,6 @@ analyzed reads, including the hidden clones.
* What is the sequence displayed for each clone ?
<<representative>>
The sequences displayed for each clone are not individual reads.
The clones may gather thousands of reads, and all these reads can have
some differences. Depending on the sequencing technology, the reads
inside a clone can have different lengths or can be shifted,
especially in the case of overlapping paired-end sequencing. There can be also
some sequencing errors.
The =.vidjil= file has to give one consensus sequence per clone, and
Rep-Seq algorithms have to deal with great care to these difference in
order not to gather reads from different clones.
For the Vidjil algorithm, it is required that the window centered on
the CDR3 is /exactly/ shared by all the reads. The other positions in
the consensus sequence are guaranteed to be present in /at least half/
of the reads. The consensus sequence can thus be shorter than some reads.
* How can I assess the quality of the data and the analysis ?
......
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