umis and clonotype of trust-barcoderep-to-10X.pl results

[xingyongma]

I used the trust-barcoderep-to-10X.pl to transform barcode_report, and got two questions:

1. Why are the numbers of umis and reads exactly the same in the results?
2. The raw_clonotype_id and raw_consensus_id are all None. Can I use turst4 to analyze and obtain clonotype information?

The command I ran run the software is as follows:
run-trust4
-f hg38_bcrtcr.fa
--ref human_IMGT+C.fa
-t 15
-u R2_001.fastq.gz
--barcode R1_001.fastq.gz
--UMI R1_001.fastq.gz
--readFormat bc:0:16,um:17:28,r1:29:-1
--barcodeWhitelist P3CB.barcode.txt.gz

[mourisl]

When using UMI, the abundance information is transformed UMI count. I think the read count information is stored, so they are the same in the output.

I think the clonotype_id in 10X's definition is not very clear. I think I saw some cases where the CDR3, V,J, C genes were the same but still had a different "Clonotype" ID. Therefore, I leave those as None. Is your downstream analysis workflow depend on this?

[xingyongma]

Thanks a lot.
Using clonotype information, my main purpose is to examine clone sizes in order to observe the expansion and contraction of clones.

[mourisl]

I think you can use the CDR3 sequence to define the clonotype.

[xingyongma]

I will have a try. And, thank you for all your quick replies.