README  (Last Updated 10/08/2020)

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INTRODUCTION
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 This README file describes the contents in this directory.

 This dataset contains raw and processed output for a PBMC sample
using the Takara SMARTer Human BCR immune profiling kit [ref here].
Matching dataset was generated using Illumina and PacBio sequencing,
with difference in Illumina library using the shorter IgG primer
and the PacBio library using the longer IgGsub primer which enables
clonotyping of the IgG subclass. 


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SAMPLE
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 [Lei & Primo, please fill this in]

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METHOD
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Library Preparation:
 [link to Primo protocol name here]

Sequencing & Runtime:
 [Lei&Primo, please fill this in]

Analysis:
 The Illumina data was processed using pRESTO and Change-O as part of the Immcantation software [3].
 The PacBio data was pre-processed using scripts at [4] followed by Change-O.

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FILE DESCRIPTION
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This dataset contains Illumina and PacBio data generated from the same RNA sample.
The PacBio dataset contains IgA/K/L/M/Gsub.
The Illumina dataset contains IgA/K/L/M/G.

The Illumina raw folder contains paired-end fastq files, separated by repertoire type.
The PacBio raw folder contains 

The Immcantation_results folder contain the clonotype output files from running
Immcantation pipeline [3]. Note that for Illumina data, pRESTO and Change-O are both run.
For the PacBio data, a PacBio-specific pre-processing step replaces the pRESTO step [4]
instead only Change-O is run.

Refer to the *run_immcantation_<platform>.sh* file in the folder for the commands 
used to generate the clonotypes.

├── Illumina
│   ├── Immcantation_results
│   └── raw
└── PacBio
    ├── Immcantation_results
    └── raw



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REFRENCES
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[1] https://www.pacb.com/research-focus/human/immunology-research/
[2] Link to Primo's BCR protocol here
[3] https://immcantation.readthedocs.io/en/stable/
[4] https://github.com/pacificbiosciences/AIRRSeq  <- Liz needs to create this

For Research Use Only. Not for use in diagnostic procedures.  Copyright 2020,
Pacific Biosciences of California, Inc. All rights reserved. The data provided in 
these files is subject to change without notice and Pacific Biosciences assumes no 
responsibility for any errors or omissions. Certain notices, terms, conditions and/or 
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