From 69d65f5abe47925f08cc9d540b02828363798ed0 Mon Sep 17 00:00:00 2001 From: Li Date: Wed, 23 Nov 2022 17:06:25 -0500 Subject: [PATCH] Update readme in scripts folder --- scripts/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/README.md b/scripts/README.md index ac2c835..3000b3b 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -10,10 +10,10 @@ Compute the clonotype diversity in a sample #### trust-cluster.py Cluster similar CDR3s based on the trust_cdr3.out or trust_report.tsv file. -#### barcode-filter.py +#### barcoderep-filter.py Filter the lowly expressed clonotype if it is identical to another highly expressed clonotype in another cell. This strategy is inspired by 10x VDJ pipeline to remove contaminations from diffused mRNAs: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/algorithms/cell-calling. -#### barcode-expand.py +#### barcoderep-expand.py Put the secondary chains in the barcode_report.tsv file in its own barcode line. This function is useful if a barcode contains multiple cells. trust-airr.pl script can then be used to create AIRR entries for the secondary chains. #### trust-barcoderep-to-10X.pl