From 866088653416eb7cf4378b68824d4c04682fe1f6 Mon Sep 17 00:00:00 2001 From: Givanna Putri Date: Thu, 16 Nov 2023 16:29:40 +1100 Subject: [PATCH] Update README.md --- README.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/README.md b/README.md index fafae00..46df2ee 100644 --- a/README.md +++ b/README.md @@ -58,6 +58,23 @@ The above parameters are pretty much the barebone requirement: * `--clone_barcodes_reference` the location of the text file containing the list of reference clone barcodes to map the reads to. * `--scrnaseq_bam_files` the location of the BAM file generated by cellranger. +## Clone barcode reference file + +This is a text file where each row represents the sequence of a clone barcode. + +It should look something like this: + +``` +CGGAGTAATACATTTTGCCT +TCGGAGTTGGCTGTCGTTTC +GTTGTCTCGGGGGGTGGAGA +CCATGATAAGGGAGTTCCGG +AGGGGAGTCGCGTGGTAGGC +TGTCTAATGGGGGTGTCACT +``` + +Generally, you will need to get this reference file from the lab that generates the lineage tracing barcode library for you. + ## Parallelisation within sample The Python package within NextClone divides reads into several