analysis code of BRILIA

BlingArida commented 5 years ago

Dear Donald Lee, We have a research subject of antibody NGS sequence,and I have found your code of BRILIA.It's difficult for me to use BRILIA because I don't have the background of matlab. Could you please help me to give me code to analysis the clone linage of my NGS sequense. And I want to get the totol AA sequence of each group.

Many thanks, Arida

BlingArida commented 5 years ago

BRILIA> runAnalysis MultiSelect.csv  Analysis
  MException with properties:

    identifier: 'MATLAB:InputParser:ParamMissingValue'
       message: 'No value was given for 'Analysis'. Name-value pair arguments require a name followed by a value.'
         cause: {0x1 cell}
         stack: [3x1 struct]

    'runAnalysis'    'MultiSelect.csv'    'Analysis'

    file: '/home/cany/.mcrCache9.2/BRILIA0/Src/CommonTools/parseInput.m'
    name: 'parseInput'
    line: 62

    file: '/home/cany/.mcrCache9.2/BRILIA0/Src/AnalysisTools/runAnalysis.m'
    name: 'runAnalysis'
    line: 16

    file: '/home/cany/.mcrCache9.2/BRILIA0/Src/BRILIA.m'
    name: 'BRILIA'
    line: 194

This is my code,is there any problems?

dleebhsai commented 4 years ago

Hi Arida, Sorry for the late reply - I changed jobs as of last year and thus am no longer in charge of updating BRILIA frequently. Are you using BRILIA as a source code in Matlab, or as stand-alone exe file? And is "MultiSelect.csv" an output of BRILIA, just renamed? If so, try to remove "Analysis" in that command and use the full path to your BRILIA output file.

BRILIA> runAnalysis "C:/Path_to_folder/MultiSelect.BRILIAv3.csv"

To do custom analysis, you'll have to make custom codes that can parse the BRILIA output .csv files, which contains the key fields: SeqNum", "ParNum", "GroupNum", "H-Seq", and "H-RefSeq". All sequences with the same GroupNum belong to the same lineage, and for each SeqNum is a ParNum (this sequence's parent SeqNum). If ParNum = 0, that means this sequence is the closest to the germline, and thus H-RefSeq is the Inferred Germline sequence. Otherwise, H-RefSeq is the sequence of the parent clone.

Can you clarify what you mean about "total AA sequence"? Did you mean the full-length AA of the VDJ gene? I'll look to see if someone at BHSAI can add in that script to expand BRILIA annotation to full-length AA. It's not included by default. If you have access to the germline sequences of V,D,J, you could write a custom script that fills in the missing DNA of the V 5' side and J 3' side.

Best, Donald

BHSAI / BRILIA

analysis code of BRILIA #14