Commit be5044fe authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/axes.md: bikeshed, details

parent d2113051
Various information are available on each clonotype, and can be show as axis.
Some of these information can also be exploited to be shown in the aligner, in the detailed informations of each clonotypes or as color by method.
Here is an unexaustive list and explanation about main availables axis:
Moreover, some axes allow to splitted clonotype by germline in scatterplot to limit the number os showed axes at the same time.
# Analysis axes
## Always present in a clonotype
Information computed on each clonotype can be show as *axes*
on the grid view, and sometimes in *columns* in the aligner and
used by the *color by* menu.
## Basic axes
* **size**: Ratio of the number of reads of the clone to the total number of reads in the selected locus
* **size (other sample)**: Ratio of the number of reads of the clone to the total number of reads in the selected locus, on a second sample
(applicable when there are several samples)
* **locus**: Locus or recombination system, as detailed [here](locus.md)
* **V/5' gene, D gene, J/3' gene**: V, D, and J genes (or 5' and 3' segments for [incomplete or special recombinations](locus.md)), regardless of the allele
* **V/5' allele, D allele, J/3' allele**: Same as above, but taking into acount each allele
* **V/5' gene**: V gene (or 5' segment), gathering all alleles
* **V/5 allele**: Same as V gene, but splitted by allele
* **D/4' gene**: D gene (or 4' segment), gathering all alleles
* **D/4 allele**: Same as D gene, but splitted by alleles
* **J/3' gene**: J gene (or 3' segment), gathering all alleles
* **J/3 allele**: Same as J gene, but splitted by alleles
* **V/5' deletions in 3'**: Number of deleted nucleotides at the 3' side of the V/5' segment
* **J/3' deletions in 5'**: Number of deleted nucleotides at the 5' side of the J/3' segment
* **locus**: Locus or recombination system
* **clone consensus length**: Length of the consensus sequence
* **clone average read length**: Average length of the reads belonging to each clone
* **clone consensus coverage**: Ratio of the length of the clone consensus sequence to the median read length of the clone. Coverage between .85 and 1.0 (or more) are good values
* **GC content**: %GC content of the consensus sequence of each clone
* **clone consensus coverage**: Ratio of the length of the clone consensus sequence to the median read length of the clone. Coverage between .85 and 1.0 (or more) are good values. See [clone coverage](user.md#clone-coverage)
* **GC content**: %GC content of the consensus sequence
* **number of samples**: Number of samples sharing the clone
* **tag**: Tag, as defined by the user with the `★` button in the [list of clones](user.md#the-list-of-clones-left-panel)
* **VIdentity IMGT**: V identity (as computed by IMGT/V-QUEST, availabe when the clonotypes have been submited there)
### N-region / CDR3 analysis
* **V/5' deletions in 3'**: Number of deleted nucleotides at the 3' side of the V/5' segment
* **J/3' deletions in 5'**: Number of deleted nucleotides at the 5' side of the J/3' segment
* **N length**: N length, from the end of the V/5' segment to the start of the J/3' segment (excluded)
* **CDR3 length (nt)**: CDR3 length, in nucleotides, from Cys104 and Phe118/Trp118 (excluded)
* **productivity**: Productivity as computed by vidjil-algo
* **productivity detailed**: Productivity detailed with non-productivity reason as "no CDR3 detected", "productive", presence of a stop-codon, seuqence out-of-frame, no-{WP}GxG-pattern. Non-productive reason are provided by the ERIC group.
* **size**: Ratio of the number of reads of each clone to the total number of reads in the selected locus
* **number of samples**: Number of samples sharing each clone
* **tag**: Tag, as defined by the user. See [user.md](user.md) XXX section The list of clones (left panel) ? XXX
## Computed depending of the options (or instance)
* **CDR3 length (nt)**: CDR3 length, in nucleotides, from Cys104 to Phe118/Trp118 (excluded)
* **productivity**: Productivity as computed by vidjil-algo (`no CDR3 detected`, `productive`, or `unproductive`
* **productivity detailed**: Same as above, but with further detail on the non-productivity cause: `stop-codon`, `out-of-frame`, `no-{WP}GxG-pattern`,
following ERIC guidelines ([Rosenquist et al., 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508071/)).
* **productivity IMGT**: roductivity (as computed by IMGT/V-QUEST, availabe when the clonotypes have been submited there)
## Other axes
Some of these values requires to have some setup on some instances of the server.
* **cloneDB occurrences**: number of occurrences in cloneDB
* **cloneDB patients/runs/sets occurrences**: "number of patients/runs/sets sharing clones in cloneDB
* **primers**: "interpolated length, between setted primers (inclusive)
* **size (other sample)**: Ratio of- the number of reads of each clone to the total number of reads in the selected locus, on a second sample
* **primers**: interpolated length, between primers (inclusive)
## Computed if some manipualtion made in the interface (primers ? )
* **productivity IMGT**: "productivity (as computed by IMGT/V-QUEST)
* **VIdentity IMGT**: "V identity (as computed by IMGT/V-QUEST)
## Table of
## Availability of axes
| name | scatterplot | in aligner | color_by |
| name | axes (grid view) | aligner | color_by |
| :----------------------- | :---------: | :--------: | :------: |
| V/5' gene | x | | x |
| V/5 allele | x | | |
| D/4' gene | x | | |
| D/4 allele | x | | |
| D gene | x | | |
| D allele | x | | |
| J/3' gene | x | | x |
| J/3 allele | x | | |
| clone consensus length | x | x | |
......
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