ExportAirr v_sequence_alignment

[gabrielathenes]

Hello,

Is there a way to have the 'v_sequence_alignment' and 'j_sequence_alignment' directly using the alignment file .vdjca and the ExportAirr function ?

Additionally, I would like to get the nucleotides of "v_sequence_alignment" and "v_germline_alignment" that belong to the cdr3, any idea on how I could do this ?

Thanks a lot !

[mizraelson]

The mixcr exportAIRR function can take a .vdjca file as input. In the AIRR format, there is no option to export the CDR3 part of the V gene. However, this can easily be done with the standard MiXCR export functions, exportAlignments for .vdjca files or exportClones for .clns/.clna files:

-nFeature {FR3End:VEnd} germline for the germline CDR3 part of the V gene
-nFeature {FR3End:VEndTrimmed} for the V part of the CDR3 in the actual clone

Example:

mixcr exportAlignments \
-nFeature {FR3End:VEnd} germline \
-nFeature {FR3End:VEndTrimmed} \
input.vdjca \
alignments.tsv

Note! It is important to use the latest develop version for this, as it contains an important fix.