Update README.md

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.