From 9bd4ac52dfc582e53b60527e8124215a2e94b984 Mon Sep 17 00:00:00 2001 From: AllonKleinLab Date: Thu, 7 Nov 2019 17:45:52 -0500 Subject: [PATCH] Update README.md --- README.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/README.md b/README.md index 307e3e5..86edaa6 100644 --- a/README.md +++ b/README.md @@ -8,11 +8,6 @@ There are three components of our code, and they need to be run in the following  - *Combining T1 T2.ipynb*, to combine clonal data from the first transplantation and second transplantation. This can be skipped if a combined dataset already exists, which is the case here.   - *clonal_annotation_T1T2_191101.ipynb*, for generating the clonal ID for a given cell. In this step, there is a parameter *dropout*. If it is set to be zero, then there is no clonal barcode dropout, and the notebook outputs data into a folder called *NoDropoutCorrection*, otherwise, the data is generated in a folder called *DropoutCorrection*.   - The clonal annotation code is adapted from the LARRY preprocessing notebook by Caleb Weinreb, but with an improved criterion for clonal clustering.  To run this notebook, there should be a folder *Combined_T1T2* in the directory of this notebook, and the following 3 files that combine the first and second transplantation dataset should be in this folder -- T1T2_cell_bcs_flat.txt: A list of cell barcodes, one barcode name for each cell -- T1T2_samp_id_flat.txt: A list of sample id's, say T1_HSC or T2_Kit, one id for each cell -- T1T2_LARRY_sorted_and_filtered_barcodes.fastq.gz: A fastq file with raw reads, obtained from target sequencing at the clonal barcode regime -In this repository, we have put in *T1T2_cell_bcs_flat.txt* and *T1T2_samp_id_flat.txt*, but not *T1T2_LARRY_sorted_and_filtered_barcodes.fastq.gz*, which is too large. This file can be accessed here:https://www.dropbox.com/s/h31y0fytmsj6zku/T1T2_LARRY_sorted_and_filtered_barcodes.fastq.gz?dl=0  ## Performing clonal analysis  Depending on which dataset to use for downstream analysis,  we can use one of the following notebooks for analyzing the clonal data, mostly for generating clonal correlations.