tcr-dist
tcr-dist copied to clipboard
phbradley
usage with mixcr files
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
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
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 GitHubhttps://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 unsubscribehttps://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 iOShttps://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 Androidhttps://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: @.***>
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
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
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
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 GitHubhttps://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 unsubscribehttps://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 iOShttps://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 Androidhttps://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: @.***>
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
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 GitHubhttps://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 unsubscribehttps://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 iOShttps://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 Androidhttps://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: @.***>
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
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/68605https://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. 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=%3E 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=%3E. You are receiving this because you are subscribed to this thread.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phbradley_tcr-2Ddist_issues_41-23issuecomment-2D1035468855&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=YyKoyzG26pxrNNYDaI2pOfMqHdnfeN0tUAxff12EESw&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABBNCH4OON6V2S73HIDFW3LU2QNQ3ANCNFSM5NXMRLXQ&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=CD6NmLyrJbLKsYXOMneR2nnUH5FzMfNH_h3vzdwGVHs&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=GITyYueE773sOzHfCsiBkXWNXrbPVXizQE57YxsqxdE&e= or Androidhttps://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=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhfEazhEXT91ASHynm_9f1N0&r=OoOdU4GyDM4g0P0UJHufcJpPOVmpY9zfZYFqEZ7QEzw&m=V29DHO2lKUJ-5tnfWbCmHRUNFC-IUBdUf35H4PMRDndQ3r91apJFIGVEeJG66Tz2&s=ToaGOBPLGW2OTnpnswUYG22g-t2wIq3KWtLEBSKjOdQ&e=. You are receiving this because you commented.Message ID: @.***>
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