Clonotype analysis with already TRUST4 data

[pyarahmadi]

Hi!

I have a TRUST4 barcode out data for TCRs with these columns "Barcode" "Type" "v_call"
"d_call" "j_call" "c_call" "cdr3" "cdr3_aa" "consensus_count"
"sequence_id" "cdr3_germline_similarity" "complete_vdj" .

Is there any way to find clonotypes in my dataset?

[PoslavskySV]

Hi, Do you have raw .fastq files?

[pyarahmadi]

Hi! Thank you for your reply. Unfortunately, no! From: Stanislav Poslavsky ***@***.***> Date: Thursday, April 6, 2023 at 13:49 To: milaboratory/mixcr ***@***.***> Cc: pyarahmadi ***@***.***>, Author ***@***.***> Subject: Re: [milaboratory/mixcr] Clonotype analysis with already TRUST4 data (Discussion #1067) Hi, Do you have raw .fastq files? — Reply to this email directly, view it on GitHub<#1067 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7ASSJ77QCDJDPBJLOCEDSTW74T5NANCNFSM6AAAAAAWV3XN7Y>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[PoslavskySV]

Well, then you can try exporting 'complete_vdj' column into .fasta file and use MIXCR generic preset to analyze it. However, I would like to suggest being cautious when interpreting the results generated by TRUST: we has observed that the output from TRUST may contain numerous spurious contigs, which either has wrong sequnece or not present in the original .fastq data at all.

[pyarahmadi]

My data is like this: <img width="390" alt="image" src="https://user-images.githubusercontent.com/130099495/230522927-1b085061-a47c-44f5-8818-224ea3a6877d.png"> Is there any way to do clonotype analysis on it? From: Stanislav Poslavsky ***@***.***> Date: Thursday, April 6, 2023 at 14:16 To: milaboratory/mixcr ***@***.***> Cc: pyarahmadi ***@***.***>, Author ***@***.***> Subject: Re: [milaboratory/mixcr] Clonotype analysis with already TRUST4 data (Discussion #1067) Well, then you can try exporting 'complete_vdj' column into .fasta file and use MIXCR generic preset<https://mixcr.com/mixcr/reference/overview-built-in-presets/#generic-bcr-amplicon> to analyze it. However, I would like to suggest being cautious when interpreting the results generated by TRUST: we has observed that the output from TRUST may contain numerous spurious contigs, which either has wrong sequnece or not present in the original .fastq data at all. — Reply to this email directly, view it on GitHub<#1067 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7ASSJ5UY4FPVDW6243T43TW74XCDANCNFSM6AAAAAAWV3XN7Y>. You are receiving this because you authored the thread.Message ID: ***@***.***>