From e63e35bfa99dfcc8c23b3ec2ecccb34ae6465259 Mon Sep 17 00:00:00 2001
From: hq <liuhq@ucsd.edu>
Date: Fri, 16 Apr 2021 17:43:57 -0700
Subject: [PATCH] Update m3c_template.ipynb

---
 .../mapping_summary_template/m3c_template.ipynb  | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/cemba_data/files/mapping_summary_template/m3c_template.ipynb b/cemba_data/files/mapping_summary_template/m3c_template.ipynb
index ae4ea9f..18e8dc8 100644
--- a/cemba_data/files/mapping_summary_template/m3c_template.ipynb
+++ b/cemba_data/files/mapping_summary_template/m3c_template.ipynb
@@ -294,7 +294,10 @@
     "reads_cutoff = 100 if miseq_guess else 500000\n",
     "low_reads = mapping_summary['FinalmCReads'] < reads_cutoff\n",
     "\n",
-    "success = ~high_mccc & ~low_reads\n",
+    "cis_long_cutoff = 5000\n",
+    "low_contacts = mapping_summary['CisLongContact'] <= cis_long_cutoff\n",
+    "\n",
+    "success = ~high_mccc & ~low_reads & ~low_contacts\n",
     "n_cell = mapping_summary.shape[0]\n",
     "n_plate = mapping_summary['Plate'].unique().size\n",
     "total_wells = n_plate * 384"
@@ -946,15 +949,6 @@
    "start_time": "2020-09-20T06:43:07.163324",
    "version": "2.1.3"
   },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "metadata": {
-     "collapsed": false
-    },
-    "source": []
-   }
-  },
   "toc": {
    "base_numbering": 1,
    "nav_menu": {},
@@ -971,4 +965,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
\ No newline at end of file