How to find out the ReadCount post Downsampling??

[MeghnaDey98]

How to generate a file containing the ReadCount field, after generating the .json files and posanalysis metrics file from downsampling, to find out the number of reads in the downsampled data?

[MeghnaDey98]

How to generate a clones.tsv file from .json file

[mizraelson]

Hi,

Could you please share the commands you've used and clarify the specific results you're aiming for?

To briefly guide you, if you run the command as shown below:

mixcr postanalysis individual \
    --metadata metadata.tsv \
    --default-downsampling count-reads-auto \
    --default-weight-function read \
    --only-productive \
    --chains IGH \
    --tables pa/pa.i.tsv \
    --preproc-tables pa/preproc.i.tsv \
    results/*.clns \
    pa/individual.json.gz

The preproc.i.tsv tables will contain information regarding the number of clones and reads after every filtering step (for entire sample), including downsampling. You can reference an example here.

Note that you cannot extract clonotype tables directly from a .json file. However, you can utilize the original .clns files to produce downsampled .clns files using mixcr downsample. Subsequently, you can execute mixcr exportClones to obtain downsampled clones in tsv tables where you will see a ReadCount value for every clone.

I hope this assists you. Please let me know if you have further questions.