Commit b509677d authored by flothoni's avatar flothoni

update doc for AIRR output

Link to #3569
parent 432b0064
Pipeline #150390 passed with stages
in 41 minutes and 33 seconds
...@@ -717,6 +717,8 @@ Using `-c designations` trigger a separate analysis for each read, but this is u ...@@ -717,6 +717,8 @@ Using `-c designations` trigger a separate analysis for each read, but this is u
| sequence | string | The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. <br />*This contains the consensus/representative sequence of each clone.* | sequence | string | The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. <br />*This contains the consensus/representative sequence of each clone.*
| rev_comp | boolean | True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. <br />*Set to null, as vidjil-algo gather reads from both strands in clones* | | rev_comp | boolean | True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. <br />*Set to null, as vidjil-algo gather reads from both strands in clones* |
| v_call, d_call, j_call | string | V/D/J gene with allele. For example, IGHV4-59\*01. <br /> *implemented. In the case of uncomplete/unexpected recombinations (locus with a `+`), we still use `v/d/j_call`. Note that this value can be null on clones beyond the `--max-designations` option.* | | v_call, d_call, j_call | string | V/D/J gene with allele. For example, IGHV4-59\*01. <br /> *implemented. In the case of uncomplete/unexpected recombinations (locus with a `+`), we still use `v/d/j_call`. Note that this value can be null on clones beyond the `--max-designations` option.* |
| feature_sequence_start, feature_sequence_end | number | Position of the start and the end of various features on the sequence. For the moment features are V, D, J and CDR3. |
| V_support, J_support | number | V gene alignment E-value measure of support for V/J gene assignment. |
| junction | string | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. <br />*null* | junction | string | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. <br />*null*
| junction_aa | string | Junction region amino acid sequence. <br />*implemented* | junction_aa | string | Junction region amino acid sequence. <br />*implemented*
| cdr3_aa | string | Amino acid translation of the cdr3 field. <br />*implemented* | cdr3_aa | string | Amino acid translation of the cdr3 field. <br />*implemented*
......
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