Postanalysis calculation for IGHV barplot

[pbpayal]

I used the postanalysis module and then exportplots to create IGHV barplot

MiXCR commands

https://mixcr.com/mixcr/reference/mixcr-postanalysis/

mixcr postanalysis individual --only-productive --metadata metadata_part1.tsv --chains IGH --tables part1_postanalysis.tsv --default-downsampling none --default-weight-function read *reassigned.clns postanalysis_part1.json

https://mixcr.com/mixcr/reference/mixcr-exportPlots/#examples_1

Export Variable gene segment families usage plot as a bar-plot by samples :

mixcr exportPlots vUsage --bar-plot-by-sample --family-usage part1_postanalysis.json part1_vUsage.pdf

Output

What is the calculation to generate the barplot ?

I chose "read" as --default-weight-function for the postanalysis step.

Is the function something like

• total number of lets say IGHV1 in sample1/total number of read counts in sample 1

Library Prep Kit

This is a SMARTer Mouse BCR IgG H/K/L Profiling Kit pairs 5' RACE kit, so I have no UMI.

Attachments

I am adding my postanalysis VgeneFamilyusage output, sample1.IGH and sample2.IGH clone output

1B_S1_L001.WT_IGH.txt

2B_S2_L001.WT_IGH.txt

part1_postanalysis.vFamilyUsage.IGH.copy.txt

[mizraelson]

Yes, if the default weight function is "read" the function is total number of reads for all clones with IGHV1 divided by the total number of reads in a given sample.

[pbpayal]

What is total number of reads for sample 1B (1B_S1_L001.WT_IGH.txt attached in previous comment) for my case?
Its it the sum of all readcounts in column 2 (readCount)?
Eg: Sample1B - 386741

[mizraelson]

Yes