Postanalysis output explanation

[pbpayal]

Hello,

I have this output for V spectratype for IGH chain from postanalysis module. I need help understanding this output.

• What is the number in the column along with the gene name?
  Eg: "60 IGHV1-64*00" - Where is the number 60 coming from?
• How are these results calculated for each gene per sample?

sample	60 IGHV1-64*00	39 IGHV1-52*00	48 IGHV1-15*00	27 IGHV6-3*00	51 IGHV1-26*00	45 IGHV1-74*00	48 IGHV1-85*00	30 IGHV8-8*00	30 IGHV1-84*00	45 IGHV10-3*00	54 IGHV3-6*00
1B.clns	20	216	42	355	386	1459	507	41	null	95	1568
2B.clns	null	163	57	47	88	467	375	5	null	null	308
3B.clns	87	255	213	8	142	149	52	null	null	219	459
4B.clns	1	325	233	44	90	86	289	null	null	94	594
5B.clns	52	86	86	null	120	117	40	null	null	27	2070
6B.clns	184	201	615	1729	727	113	384	142	20	34	2819
7B.clns	169	28	152	76	506	1245	263	759	null	28	680
8B.clns	291	2909	1328	1	737	152	71	55	3	173	12
9B.clns	null	15	311	30	230	244	565	85	null	20	92

Similarly, for CDR3Spectratype output for IGH from postanalysis module, what is the number 45 in "45 CARDRYYSRAAMDYW" ? And what is "45 null" in 4th column?

sample	45 CARDRYYSRAAMDYW	45 CAREGHYYGSVFDYW	45 null	42 CFYYYGSSYYFDYW	42 null	39 CARHNYYGSFDVW	39 CARPAQGAWFAYW	39 null	36 CARFATGGFDYW
1B.clns	null	null	48382	null	39527	null	null	27714	null
2B.clns	null	null	16026	null	17547	null	null	11306	null
3B.clns	null	null	23383	null	36835	null	null	27831	null
4B.clns	null	null	17355	null	22524	null	null	16896	null
5B.clns	null	null	24090	null	35170	null	null	20702	null
6B.clns	null	null	57382	null	68437	null	null	45770	null
7B.clns	null	null	46346	null	69584	null	null	49402	null
8B.clns	2634	3664	38413	5939	31456	2326	4461	40400	3457
9B.clns	null	null	20380	null	22727	null	null	17179	null

I would really appreciate if you could point me to the explanation and calculation behind the postanalysis module results.

Thanks

[mizraelson]

Hi, can you please specify the version of MiXCR you used and the exact command.

[pbpayal]

I used mixcr/4.6.0

I used the postanalysis module -
mixcr postanalysis individual --only-productive --metadata part1_metadata.csv --chains IGH --tables part1_postanalysis.tsv --default-downsampling none --default-weight-function read **reassigned.clns postanalysis_part1.json

[mizraelson]

Thank you. The number in both tables is the length of the CDR3 region in nucleotides.

• The first table shows the distribution in reads of every V gene for each CDR3 region length.
• The second table shows the presence of different CDR3 lengths in each sample. The nucleotide sequence is shown only for the top ten most abundant clones.

To answer your questions directly:

• "60 IGHV1-64*00" refers to the number of reads for clones with IGHV1-6400 and a CDR3 length of 60 nucleotides.
• "45 CARDRYYSRAAMDYW" refers to the number of reads for clones with the following CDR3 sequence (CARDRYYSRAAMDYW), which is 45 nucleotides long and is one of the top 10 most abundant.
• "45 null" refers to the total number of reads for all clones with a CDR3 sequence that is 45 nucleotides long (including CARDRYYSRAAMDYW)

[JoostKoedijk]

Hi mizraelson, Thanks a lot for your answer! I have a question about the most abundant clones shown. You mentioned that the "45 CARDRYYSRAAMDYW" is one of the top 10 most abundant clones. The most abundant clone out of: all clones that are 45 nucleotides long? Or all clones detected?

In my data, I usually have around 2-6 clones with the CDR3 sequence for a given nucleotide length + 'the nucleotide length null' which is much higher than the sum of the clones with the same nucleotide length.

Many thanks in advance!

[mizraelson]

45 CARDRYYSRAAMDYW:

The sequence CARDRYYSRAAMDYW is among the top 10 most abundant clones detected (regardless of length).