usage with mixcr files

[guillemsanchezsanchez1996]

usage with mixcr files

[phbradley]

Hi Guillem, Can you provide an example of the format of your input files? Do you have gene expression data or is this just TCR sequences? Take care, Phil

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________________________________ From: guillemsanchezsanchez1996 ***@***.***> Sent: Monday, February 7, 2022 5:05 AM To: phbradley/tcr-dist ***@***.***> Cc: Subscribed ***@***.***> Subject: [phbradley/tcr-dist] usage with mixcr files (Issue #41) Dear Phil, After reading your paper I would be interested in checking identifying shared motifs in a particular subset of sorted T cells that undergo strong TCR signaling during their development in thymus. I'm quite new with python and I have been able to set up the enviroment and installl packages and all dependecies in windows using WSL. Unfortunately I have only single chain files (alpha and beta) from several subjects. Is there a way I can adapt the input to perform the analysis only with single chain files? Thanks in advance for your help :) Guillem Sanchez — Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phbradley_tcr-2Ddist_issues_41&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=DeBGJQHMHRH-J6vpIH-OH2VPod3jy8zzMagKqbFW5nMWLFZfSRb5bSCo9Wi5-H8W&s=TgMkA3McRpwvtVFTTWDpACWe_J0e9wPSikSpZiwi4AE&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABBNCH43S3PH72OMF6S3OW3UZ67RLANCNFSM5NXMRLXQ&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=DeBGJQHMHRH-J6vpIH-OH2VPod3jy8zzMagKqbFW5nMWLFZfSRb5bSCo9Wi5-H8W&s=TO9Tm6-mt0LwO0Kbx7YWZ5P2z-RyHmvdc3N4YC_XihI&e=>. Triage notifications on the go with GitHub Mobile for iOS<https://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=DeBGJQHMHRH-J6vpIH-OH2VPod3jy8zzMagKqbFW5nMWLFZfSRb5bSCo9Wi5-H8W&s=FJmQepC8b8KAt7-DOxoyZSvpFMjQ4WXG3cxAAnPyK64&e=> or Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=DeBGJQHMHRH-J6vpIH-OH2VPod3jy8zzMagKqbFW5nMWLFZfSRb5bSCo9Wi5-H8W&s=-bBi6U0CLY4kHRCN2c6ypdjoHdeUIaS3r8NdV6lR-n0&e=>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[guillemsanchezsanchez1996]

Dear Phil,
Thanks a lot for your fast answer! I have only TCR sequence
AB1A.txt
This is an example of a Mixcr processed file, as you can see same clones are pooled in the same rows.
One can also convert it to vdjtools file and simplify quite a lot the output, but the principle is the same (rows with accumulated counts of the distinct single chains).
NFF.AB1A.txt
Hope it helps,

Guillem

[guillemsanchezsanchez1996]

Hello again Phil,
Do you think is it feasable to try to transform these vdjtools/mixcr files? Or you think this single chain data cannot be used in your package to search cdr3 motifs?

Best,
Guillem

[phbradley]

Hi Guillem, One more follow-up question: how many TCRs are you looking to analyze? Three other tools that might be more appropriate for single-chain data are * ALICE (Walczak lab) * TCRnet (from VDJtools folks) * GLIPH2 (Davis Lab) Take care, Phil

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________________________________ From: guillemsanchezsanchez1996 ***@***.***> Sent: Thursday, February 10, 2022 4:19 AM To: phbradley/tcr-dist ***@***.***> Cc: Bradley PhD, Phil ***@***.***>; Comment ***@***.***> Subject: Re: [phbradley/tcr-dist] usage with mixcr files (Issue #41) Hello again Phil, Do you think is it feasable to try to transform these vdjtools/mixcr files? Or you think this single chain data cannot be used in your package to search cdr3 motifs? Best, Guillem — Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phbradley_tcr-2Ddist_issues_41-23issuecomment-2D1034856858&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=uxH46QEeMaq8gPM8WVe-cKMPn8e212722YCRJV361-fS6YJ-DbGEDjKLK0W2ywkr&s=EbWWwgYBBCFXD7FUQ9Nv7ZrdoeW6dR4dmzsELpt05bc&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABBNCH7QFE56JZJ2LTINOA3U2OUNRANCNFSM5NXMRLXQ&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=uxH46QEeMaq8gPM8WVe-cKMPn8e212722YCRJV361-fS6YJ-DbGEDjKLK0W2ywkr&s=lx3tLgA3xlxGD2Q292r8iW_RMHiklD5ihp6tG_2xkZs&e=>. Triage notifications on the go with GitHub Mobile for iOS<https://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=uxH46QEeMaq8gPM8WVe-cKMPn8e212722YCRJV361-fS6YJ-DbGEDjKLK0W2ywkr&s=zfOQ4ObhErgEYJ0UT53rrS4xRIMJTjhGjhMH4nwAibc&e=> or Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=uxH46QEeMaq8gPM8WVe-cKMPn8e212722YCRJV361-fS6YJ-DbGEDjKLK0W2ywkr&s=hnMqc5rjF7c4u4sx1jICdndFjWQAqyux96L7uiqK57s&e=>. You are receiving this because you commented.Message ID: ***@***.***>

[guillemsanchezsanchez1996]

Dear Phil,
Thanks for the suggestions
I have 12 samples with around 100 to 500 TCR sequences. Do you think is it feasable? Is there a way to adapt the output lf mixcr to the input data for tcr-dist
Guillem

[agartland]

Hi Guillem You may also want to take a look at tcrdist3, which is more flexible with its inputs and can do many of the same kinds of analyses. All best, Andrew https://tcrdist3.readthedocs.io/en/latest/ https://elifesciences.org/articles/68605 From: guillemsanchezsanchez1996 ***@***.***> Sent: Thursday, February 10, 2022 10:54 AM To: phbradley/tcr-dist ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [phbradley/tcr-dist] usage with mixcr files (Issue #41) Dear Phil, Thanks for the suggestions I have 12 samples with around 100 to 500 TCR sequences. Do you think is it feasable? Is there a way to adapt the output lf mixcr to the input data for tcr-dist Guillem — Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phbradley_tcr-2Ddist_issues_41-23issuecomment-2D1035337309&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=50WpYp3DCk77w54dOCIpzD-ckOg1vpeQIBUKqxnaMVI&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AA5QYJVI4MWNXLX2PKGBD23U2QCT5ANCNFSM5NXMRLXQ&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=Q6NiO-dyy4vE2bLWymlBj9TbyrQVgT8fRuin9GYy48k&e=>. Triage notifications on the go with GitHub Mobile for iOS<https://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=xrgob_2zuVrH7EixHLeLSrb8Fu0n1iQz8_mtiFHHvR0&e=> or Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=DbHuYrsNe4OPX6hAjzfF5V60VicOUMESqFITefe1CUg&e=>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[phbradley]

Yes! Oh, I just now realized that this was not a "conga" question but a "tcrdist" question. Sorry, Guillem, I have been getting many github emails about a different software project, and I was interpreting your email as pertaining to that one. For tcrdist-type analyses, tcrdist3 is absolutely the way to go, and as Andrew said it has some very flexible I/O. I'm sorry for not realizing my mistake earlier. Take care, Phil

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________________________________ From: Andrew Fiore-Gartland ***@***.***> Sent: Thursday, February 10, 2022 12:26 PM To: phbradley/tcr-dist ***@***.***> Cc: Bradley PhD, Phil ***@***.***>; Comment ***@***.***> Subject: Re: [phbradley/tcr-dist] usage with mixcr files (Issue #41) Hi Guillem You may also want to take a look at tcrdist3, which is more flexible with its inputs and can do many of the same kinds of analyses. All best, Andrew https://tcrdist3.readthedocs.io/en/latest/<https://urldefense.proofpoint.com/v2/url?u=https-3A__tcrdist3.readthedocs.io_en_latest_&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=fUVMmUOCfD2hagRxevYoBZgM--KVJMBEWvohnHnjulQ&e=> https://elifesciences.org/articles/68605<https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_68605&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=gKim_OVi4X4fSmECAUScPw4SxwXaWE8Q238sP9VTGFg&e=> From: guillemsanchezsanchez1996 ***@***.***> Sent: Thursday, February 10, 2022 10:54 AM To: phbradley/tcr-dist ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [phbradley/tcr-dist] usage with mixcr files (Issue #41) Dear Phil, Thanks for the suggestions I have 12 samples with around 100 to 500 TCR sequences. Do you think is it feasable? Is there a way to adapt the output lf mixcr to the input data for tcr-dist Guillem — Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phbradley_tcr-2Ddist_issues_41-23issuecomment-2D1035337309&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=50WpYp3DCk77w54dOCIpzD-ckOg1vpeQIBUKqxnaMVI&e=%3E, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AA5QYJVI4MWNXLX2PKGBD23U2QCT5ANCNFSM5NXMRLXQ&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=X10ZT7WaHRZ-eVSDqT5PSJJy-dt-EQ_Q6fSKRknQmmQ&m=FrOo1uy3pc7_4Qlwst0PaAs0PxmZw-Edh__NdEFK1zomuSG85fgVHDYx9nNogxef&s=Q6NiO-dyy4vE2bLWymlBj9TbyrQVgT8fRuin9GYy48k&e=%3E. 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[guillemsanchezsanchez1996]

Dear Andrew and Phil,
Thank you both for your suggestions. I was awared of tcrdist3 and I managed to run several functions with my data. I was interested in tcr-dist basically because of the nice tree representation of the cdr3 motifs that you do in your paper of 2017.

Best
Guillem