Data Load - Rhapsody

[martuskaR]

Hello,

I am new to R and Immunarch.
I would like to analyse TCRseq data from BD Rhapsody protocol. The data is a csv file, and looks like this:

When I load it with repLoad(), there is no error, however, the list is empty. How can I load my file successfully?

Thanks a lot for your help in advance :)

[Alexander230]

Hello, @martuskaR!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

Unfortunately, it's not possible to load BD Rhapsody output files into Immunarch, because they don't contain nucleotide sequences for chains, which are necessary for Immunarch functions to work. You can try to load data from earlier stage of pipeline, before processing it in BD Rhapsody, to have an input file that contains nucleotide sequences.

Best regards,
Aleksandr

[martuskaR]

Hello Alexander,
Than you very much for your reply.
The file contains nucleotide sequence for alpha CDR3 and beta CDR3. Is that not sufficient?
Are you planning on adding rhapsody format into your package?

I am trying to get it to work in 10X format which has worked for a single chain data. When I input reads for alpha and beta chains with a semicolon e.g. TRGV401 ; TRDV101 (same fro nt and aa sequences), the data is not read and no clones are found (for single chain data I have 3k clones). Could you advise on this, what am I doing wrong?

Best,

--

--

[Alexander230]

You can try to export to AIRR format from BD Rhapsody; it can work with Immunarch if the data contains full sequences (not just CDR3). We are now working to add full single cell / multi chain data support to Immunarch; now it is in beta. Could you, please, send an example of 10x data that isn't loaded in Immunarch correctly?

Best,
Aleksandr

[martuskaR]

Thanks a lot. Sure, below is may data transformed (or at least attempted) into a 10X format.

There is no error, however, the 'data' has no rows (0x32).

Best,

[Alexander230]

Can you, please, send the file that you get after the transformation? I can check what's happening and probably can fix the file to make it load successfully.

Best regards,
Aleksandr

[martuskaR]

Dear Aleksandr, Thank you very much fir offering me your help. The file is attached above. I am also uploading the Rhapsody format, original file that we get from Seven Bridges (CD3_VDJ.csv). Thanks a lot, Kind Regards, Marta From: Aleksandr Popov ***@***.***> Date: Tuesday, 31 January 2023 at 15:35 To: immunomind/immunarch ***@***.***> Cc: Marta Rzepkowska ***@***.***>, Mention ***@***.***> Subject: Re: [immunomind/immunarch] Data Load - Rhapsody (Discussion #344) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Can you, please, send the file that you get after the transformation? I can check what's happening and probably can fix the file to make it load successfully. Best regards, Aleksandr — Reply to this email directly, view it on GitHub<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fimmunomind%2Fimmunarch%2Fdiscussions%2F344%23discussioncomment-4831292&data=05%7C01%7Cmarta.1.rzepkowska%40kcl.ac.uk%7C9bb8d00f87064e2f9bfe08db03a0bc5c%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638107761107533914%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I26ACCUmSA8Bl2%2FF1VQYEXRvWHoLO0JeAbq%2FZxPj2Lg%3D&reserved=0>, or unsubscribe<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA5DQJ3DL3HVWIQAXADUO3QLWVEWKZANCNFSM6AAAAAAUGFQU6A&data=05%7C01%7Cmarta.1.rzepkowska%40kcl.ac.uk%7C9bb8d00f87064e2f9bfe08db03a0bc5c%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638107761107533914%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HZxhT3TOUC6agWaTkjslg8Vdjzj2TN%2FvggRDTBWxMZE%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Alexander230]

Hello, Marta!

I don't see any attachments in this thread, only 2 png screenshots. You can drag and drop a file into GitHub message window to attach it to the message, so I will be able to download it.

Kind regards,
Aleksandr

[martuskaR]

10x_VDJ.csv
CD3_VDJ.csv

Hello Aleksandr,

Thank you so much for following up. I hope the files are attached successfully now!

Best Regards,
Marta

[Alexander230]

Yes, 10x_VDJ is parsed as empty, I will check what's missing and then find out how to update this file to load it successfully.

Best regards,
Aleksandr

[martuskaR]

That’s very kind, thank you so much. Regards, Marta From: Aleksandr Popov ***@***.***> Date: Thursday, 2 February 2023 at 17:03 To: immunomind/immunarch ***@***.***> Cc: Marta Rzepkowska ***@***.***>, Mention ***@***.***> Subject: Re: [immunomind/immunarch] Data Load - Rhapsody (Discussion #344) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Yes, 10x_VDJ is parsed as empty, I will check what's missing and then find out how to update this file to load it successfully. Best regards, Aleksandr — Reply to this email directly, view it on GitHub<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fimmunomind%2Fimmunarch%2Fdiscussions%2F344%23discussioncomment-4853891&data=05%7C01%7Cmarta.1.rzepkowska%40kcl.ac.uk%7C4ee3439db0b74724c72308db053f7267%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638109542291826555%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BSFiPwG8GkAUh%2BqMTKHxpwn6Lv04mhc4tHnirQtH3d4%3D&reserved=0>, or unsubscribe<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA5DQJ3E727X36X56YJRURWDWVPSHDANCNFSM6AAAAAAUGFQU6A&data=05%7C01%7Cmarta.1.rzepkowska%40kcl.ac.uk%7C4ee3439db0b74724c72308db053f7267%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638109542291826555%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QNJUudrLgb3LK1DHwEkm2EJ8Jwk6JNApv1N6s7ySzR0%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Alexander230]

Checked it, looks like all sequences in CDR3.aa column are non-coding and were filtered out, and when I use repLoad() with argument .coding = FALSE, the file loaded successfully. Immunarch doesn't support ; character in CDR3 column, better to keep only the 1st sequence in it; but probably, a lot of sequences in these data will still translate as non-coding.

Now we are working on better single cell support; the next version of Immunarch will have a separate column for each chain, without separating data with ; character within a column.

Best regards,
Aleksandr

[martuskaR]

Hello again,

I am facing an issue this time as well. I am using TCR seq files from BD Rhapsody. I downloaded AIRR standard .tsv file with my data and although it seems to load fine, the column 'Barcode' is missing. I cannot run any function successfully, and without grouping by clusters from my Seurat object, I won't be able to do any analysis.

Thanks a lot, your help will be much appreciated!
VDJmerged.tsv.zip