Update README.md

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).
+## 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 [email protected] ☕️