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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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Link of Alignment-file and Clone-file #113

Closed relastle closed 8 years ago

relastle commented 8 years ago

I understand the mapping between initial reads and final clonotypes. But I want to know the mapping between Aligned sequence and clones.

dbolotin commented 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?

relastle commented 8 years ago

sorry, i mean the latter.

the map such as clone_id -> [seq_id1, seq_id2, ...., seq_idN] .

PoslavskySV commented 8 years ago

@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?

relastle commented 8 years ago

thank you! That works well.