Closed relastle closed 8 years ago
Could you please explain in some more details desired output/type of information you want to get from MiXCR? If I get you right you want to export alignments for the specified clonotype? Or you just want some kind of id to id mapping?
sorry, i mean the latter.
the map such as clone_id -> [seq_id1, seq_id2, ...., seq_idN] .
@3sevieria did you look into these docs https://mixcr.readthedocs.io/en/latest/export.html#exporting-reads-aggregated-by-clones ? From your last answer it seems that all you need is already in MiXCR. You can pass the option --index
and then retrieve clone -> readId
mapping in e.g. the following way:
mixcr assemble --index index_file alignments.vdjca output.clns
mixcr exportClones -p min -readIds index_file clones.clns clones.txt
which will give you smth like
Clone ID Clone count Best V hit ... Reads
0 7213 IGHV4-34*00 ... 56,74,92,96,101,119,169,183...
1 2951 IGHV2-23*00 ... 46,145,194,226,382,451,464...
2 2269 IGHV4-34*00 ... 58,85,90,103,113,116,122,123...
... ... ...
If you need something more, could you please explain it in more detail?
thank you! That works well.
I understand the mapping between initial reads and final clonotypes. But I want to know the mapping between Aligned sequence and clones.