From ff670943501f8e42d742016e1212b4a50bac5789 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 3 Jun 2022 11:24:36 -0500 Subject: [PATCH 1/2] update headers --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6973481..0f9c136 100644 --- a/README.md +++ b/README.md @@ -84,9 +84,9 @@ Rscript junc_calling_script.R \ ``` Final ouptput: Counts matrix with each row as a junction and each column as a cell, metadata containing junction information, including gene, transcript ID, and chromosomal location. -### Annotation of Intron Junctions +### Annotation of Junctions -Annotation of intron junctions identified in sample. +Annotation of junctions identified in sample. Here the reference gtf is used to classify each 5' and 3' end of the intron. Output will add on additional columns to the metadata table including startClass and endClass, classifying the junction ends as the canonical (main) or alternative (not_main_3_prime/not_main_5_prime) end. Events will also be classified as exon skipping events or alternative splicing events. @@ -143,7 +143,7 @@ Rscript strand_adjustment.R \ ``` -#### Option A: Individual Patient +#### Option A: Individual Samples 2. Run Differential transcript usage analysis. This requires the strand adjusted metadata matrix, full counts matrix from intron junction calling, and a table with cell barcodes, genotype information, and cell type assignment (produced from short read data analysis using GoT). From afbf83f26f0b1889b87a0ff542672453b146c4fd Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 3 Jun 2022 11:33:32 -0500 Subject: [PATCH 2/2] update doctoc --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 0f9c136..0bac217 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,9 @@ - [Reference files and general setup](#reference-files-and-general-setup) - [GoT-Splice Pipeline overview](#got-splice-pipeline-overview) - [Junction Calling in Single Cells](#junction-calling-in-single-cells) - - [Annotation of Intron Junctions](#annotation-of-intron-junctions) + - [Annotation of Junctions](#annotation-of-junctions) - [Differential Transcript Usage](#differential-transcript-usage) - - [Option A: Individual Patient](#option-a-individual-patient) + - [Option A: Individual Samples](#option-a-individual-samples) - [Option B: Combine Samples](#option-b-combine-samples) - [Option C: Within Cell Types/ Clusters](#option-c-within-cell-types-clusters) - [Running the full GoT-Splice pipeline](#running-the-full-got-splice-pipeline)