From d041753eb39cf0a196205df1e7b1b1d313d4988d Mon Sep 17 00:00:00 2001 From: "Erica Y. Scott" Date: Wed, 25 Mar 2020 12:17:21 -0400 Subject: [PATCH] Update README.md --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index dbf6bb0..8613c4a 100644 --- a/README.md +++ b/README.md @@ -4,18 +4,18 @@ The laser lysis capture method implemented in DISCO offers spatially and tempora Each cell has a barcode incorporated into Read 1, making the cell's transcriptome accountable and traceable through the pipeline. This barcode includes a unique cell barcode (12bp) and a UMI (8bp), the first part of our bioinformatic pipeline deals with parsing these. ## General Worlflow -The provided scripts go through mapping, parsing fasta headers (barcodes and UMIs), generating count data, making figures and performing differential gene expression (DGE): -1. -2. -3. -4. -5. -FigureScripts: -DependentScripts: +The provided scripts go through mapping, parsing fasta headers (barcodes and UMIs), generating count data, making figures and performing differential gene expression (DGE): \n +1. Append Read1 barcode information to Read2 fasta header \n +2. Align with Star Aligner \n +3. Collapse redundant UMIs \n +4. Parse and separate unique cell barcodes \n +5. Gather gene count data (FeatureCounts) \n +RFigureScripts: TPM normalization, figure generation, DGE with EdgeR, UMAP implementation \n +DependentScripts: FeatureCounts and barcode demuliplexing scripts. ## Publication pending ### Authors of scripts -Erica Y. Scott: Scripts 1-5 and Figure scripts 1-6 +Erica Y. Scott: Scripts 1-5 and Figure scripts 1-7 \n Harrison Edwards: python barcode parser scripts within DependentScripts/ -- GitLab