deciphering query results

CSree commented 3 days ago

Hi after running the query against the ref database, I get the file with the results. However the antigen column reads "COVID19:ADIRP0000356_TCRB.tsv", and so on. How do I access this tsv file Thank you Chai

s175573 commented 3 days ago

Hello Chai,

I've uploaded this file to the data folder. Please check.

Thanks, Bo

From: CSree @.> Sent: Wednesday, October 16, 2024 1:13 PM To: s175573/GIANA @.> Cc: Subscribed @.***> Subject: [External][s175573/GIANA] deciphering query results (Issue #12)

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Hi after running the query against the ref database, I get the file with the results. However the antigen column reads "COVID19:ADIRP0000356_TCRB.tsv", and so on. How do I access this tsv file Thank you Chai

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CSree commented 2 days ago

Hi Bo thanks for the prompt response, I was able to access the file. I have a few qns which I should have asked before the prev one. So I queried a file, against the Ref_Cancer_Covid_MS database. I put the clustered file for both in the same dirs as the main file. I got 3 files as output:

tmp_query--RotationEncodingBL62.txt : within GIANA dir, this has fewer sequences than the input file, clustered by GIANA, ref column has entries ref and query.
tmp_query.txt : within GIANA dir, this has several more sequences than in the input file, no giana clusters, and query col has ref and query entries.
_query_Ref_Cancer_Covid_MS.txt : this is in the output folder specified by me, it has few sequences, and the final column has only query in the entries.

How am I to interpret each file, I also notice that there are sequences in these files that are not present in the input file. I understand the ones that are fused with the reference , however even among the sequences that are listed as query in the final column, there are many that are not there in the input file.

Please help me understand this, and which is the final file I can utilize for further analysis. Thanks in advance. Chai

s175573 commented 2 days ago

Only the last file is for final processing. The tmp_* files are intermediate and should be ignored.

Thanks, Bo

From: CSree @.> Sent: Thursday, October 17, 2024 12:58 PM To: s175573/GIANA @.> Cc: Li, Bo @.>; Comment @.> Subject: [External]Re: [s175573/GIANA] deciphering query results (Issue #12)

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Hi Bo thanks for the prompt response, I was able to access the file. I have a few qns which I should have asked before the prev one. So I queried a file, against the Ref_Cancer_Covid_MS database. I put the clustered file for both in the same dirs as the main file. I got 3 files as output:

tmp_query--RotationEncodingBL62.txt : within GIANA dir, this has fewer sequences than the input file, clustered by GIANA, ref column has entries ref and query.
tmp_query.txt : within GIANA dir, this has several more sequences than in the input file, no giana clusters, and query col has ref and query entries.
_query_Ref_Cancer_Covid_MS.txt : this is in the output folder specified by me, it has few sequences, and the final column has only query in the entries.

How am I to interpret each file, I also notice that there are sequences in these files that are not present in the input file. I understand the ones that are fused with the reference , however even among the sequences that are listed as query in the final column, there are many that are not there in the input file.

Please help me understand this, and which is the final file I can utilize for further analysis. Thanks in advance. Chai

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CSree commented 2 days ago

Oh ok. Since it has no sequences with ref in the last column, does that mean that none of the sequences matched with any in the reference? It has >125,000 tcr sequences form one patient with covid, I thought a good percentage of them should have matched. Chai

s175573 commented 2 days ago

How many sequences are there in your reference data?

Thanks, Bo

From: CSree @.> Sent: Thursday, October 17, 2024 1:30 PM To: s175573/GIANA @.> Cc: Li, Bo @.>; Comment @.> Subject: [External]Re: [s175573/GIANA] deciphering query results (Issue #12)

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Oh ok. Since it has no sequences with ref in the last column, does that mean that none of the sequences matched with any in the reference? It has >125,000 tcr sequences form one patient with covid, I thought a good percentage of them should have matched. Chai

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CSree commented 2 days ago

I used the first in the list : HC100_COVID300_HNSC_MMR_PDA_OV_Page_BrainMet_LungMDA_melanoma_CRC_DC_RCC_Bladder_Cervical_Riaz_MS--RotationEncodingBL62.txt

found here: https://zenodo.org/records/4698929

It has 10,285,868 sequences pertaining to multiple diseases including COVID, cancer, Multiple sclerosis, etc.

s175573 commented 2 days ago

Can you paste the first 100 lines of your query TCR file? It is strange that none clustered with the ref.

Thanks, Bo

From: CSree @.> Sent: Thursday, October 17, 2024 2:17 PM To: s175573/GIANA @.> Cc: Li, Bo @.>; Comment @.> Subject: [External]Re: [s175573/GIANA] deciphering query results (Issue #12)

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I used the first in the list : HC100_COVID300_HNSC_MMR_PDA_OV_Page_BrainMet_LungMDA_melanoma_CRC_DC_RCC_Bladder_Cervical_Riaz_MS--RotationEncodingBL62.txt

found here: https://zenodo.org/records/4698929

It has 10,285,868 sequences pertaining to multiple diseases including COVID, cancer, Multiple sclerosis, etc.

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CSree commented 2 days ago

Here it is: first 150

peptide | tcrbv

s175573 commented 2 days ago

Your TRBV gene name format doesn't match the reference data. Please fix this according to the criteria in this code:

https://github.com/s175573/GIANA/blob/master/ProcessAdaptiveFile.R

Thanks, Bo

From: CSree @.> Sent: Thursday, October 17, 2024 3:57 PM To: s175573/GIANA @.> Cc: Li, Bo @.>; Comment @.> Subject: [External]Re: [s175573/GIANA] deciphering query results (Issue #12)

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Here it is: first 150

peptide | tcrbv

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s175573 / GIANA

deciphering query results #12