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Commit a0da52ec authored by Wazali's avatar Wazali
Browse files

doc/ What is the sequence displayed for each clone ?

Question from AF (Rennes), translating answer from @mikael-s
parent ddb95672
......@@ -107,6 +107,7 @@ Otherwise, such .vidjil files can be obtained:
them either in the list, the graph or the scatterplot, or by drawing a
rectangle around clones to be selected in the scatterplot view), you can
view their sequences in the aligner.
- See "What is the sequence displayed for each clone ?" below
- Sequences can be aligned together to see how they differ or how similar
they are (“align” button). After aligning them a shaded background identifies
substitutions and a dash identifies indels.
......@@ -200,6 +201,25 @@ analyzed reads, including the hidden clones.
* What is the sequence displayed for each clone ?
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 to not 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 ?
To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled.
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