From 93d5431578fa233a70eec6dd3ab38dbbe2b5aaff Mon Sep 17 00:00:00 2001 From: Yang Xie Date: Fri, 15 Mar 2024 22:59:09 -0700 Subject: [PATCH] Update README.md --- 02.analysis/README.md | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/02.analysis/README.md b/02.analysis/README.md index c7c678c..bb5c491 100644 --- a/02.analysis/README.md +++ b/02.analysis/README.md @@ -1,9 +1,2 @@ -## Preprocessing workflow -We used [scHiCluster](https://github.com/zhoujt1994/scHiCluster) to impute single cell contacts matrices, and performed domain calling as well as loop calling. In details, -1. Fastq are processed, mapped and convert to pairs file using [04.proc_paired_hic_v2.1.sh](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/04.proc_paired_hic_v2.1.sh). -2. High quality cells are selected using the notebook [01.cell_filtering.ipynb](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/01.cell_filtering.ipynb). -3. Contacts information from individual cells are extracted using scripts [phc.sc_splitPairs_v2.py](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/phc.sc_splitPairs_v2.py). -4. Imputation is carried out for individual cells using [schic_impute_v2.sh](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/schic_impute_v2.sh). -5. Single cell GAD score is calculated using [schic_gene_score_v2.sh](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/schic_gene_score_v2.sh). This allows us to perform embedding and cell types annotation. -6. Single cell insulation score and domain calling are done using [schic_domain_v2.sh](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/schic_domain_v2.sh). -7. Loops calling for each cell cluster is done using [schic_loops_v3.sh](https://github.com/Xieeeee/Droplet-Hi-C/tree/main/01.pre-process/scripts/schic_loops_v3.sh). \ No newline at end of file +## Analysis workflow +Analysis notebook to reproduce panels in main figures in our manuscript can be found in this directory. If you found any scripts or code are missing, feel free contact me at y2xie@ucsd.edu ☕️