The majority of results in 'clones_TR[A|B].tsv' are "region_not_covered"

[ChoiJi-Hye]

Hi!
Thanks for creating a great tool!

Expected Result

I used [TakaRa] SMART-Seq Human TCR (with UMIs) to generate bulk TCR data and used your tool for analysis, but most of the results came out as "region_not_covered."
When I look at other people's results, most of them seem to have sequences written. Is there an option I might have missed?

I proceeded with the analysis using takara-human-rna-tcr-umi-smartseq, but is this an accurate result?
Are there any other issues?

Actual Result

Exact MiXCR commands

Mixcr_4.6.0/mixcr analyze takara-human-rna-tcr-umi-smartseq R_23_00645_FN_ETC_RNA_R1.fastq.gz R_23_00645_FN_ETC_RNA_R2.fastq.gz result_directory/R_23_00645 -t 16

MiXCR report files

Thank you for your help!
Ji-Hye Choi

[mizraelson]

The command seems correct. It appears that the issue is with the data itself. Could you please share the pair of raw FASTQ files? I can then review them and provide some insights. You can reach us at support@milaboratories.com

[mizraelson]

Thank you for sharing the data. It appears that there is an issue with the read length. By default, the preset expects sequencing of 300+300, in accordance with the manufacturer's recommendations. In your case, with reads of 150+150, the reads do not fully cover the VDJ region. Please add the parameter --assemble-clonotypes-by CDR3 to assemble clones by the CDR3 region instead of by the full-length sequence.

[ChoiJi-Hye]

Thank you so much for your help!

Following your advice, I was able to increase the read count in the result files and obtain both the nucleotide and amino acid sequences for the CDR3 region.

I really appreciate your quick assistance!