update

docs/conf.py

@@ -16,6 +16,11 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import os
+
+# Define the canonical URL if you are using a custom domain on Read the Docs
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
 
 # -- Project information -----------------------------------------------------
 
@@ -130,6 +135,11 @@
   'github_repo': 'continuous-sphinx',
   'github_version': 'master/source/'
 }
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True
 
 html_js_files = ['https://cdn.jsdelivr.net/npm/handsontable/dist/handsontable.full.min.js']
 html_css_files = ['https://cdn.jsdelivr.net/npm/handsontable/dist/handsontable.full.min.css']

docs/content/NGS_pipelines/leafcutter.rst

@@ -0,0 +1,56 @@
+Differential RNA splicing analysis
+==================================================
+
+Summary
+^^^^^^^
+
+Differential splicing analysis using leafcutter, one of the best tools.
+
+Only works for hg19.
+
+Only works for paired-end RNA-seq data.
+
+
+Input
+^^^^^
+
+Example data dir: Projects/Siqi_data/RNAseq_data/Differential_Exon_Analysis/test
+
+1. fastq.tsv
+----------
+
+Use ``run_lsf.py --guess_input`` to generate.
+
+
+2. design.tsv
+----------------
+
+Two columns. First column should match to the labels in ``fastq.tsv``. Second col is the group. Only pairwise. From leafcutter: ``Additional columns can be used to specify confounders, e.g. batch/sex/age. Numeric columns will be treated as continuous, so use e.g. batch1, batch2, batch3 rather than 1, 2, 3 if you a categorical variable.``
+
+::
+
+	2393110_Nontarget_Hudep2_2	WT
+	2393109_Nontarget_Hudep2_1	WT
+	2393111_Nontarget_Hudep2	WT
+	2393114_M1_Hudep2	sgRNA
+	2393113_M1_2_Hudep2_2	sgRNA
+	2393112_M1_2_Hudep2_1	sgRNA
+
+
+Usage
+^^^^^
+
+.. code:: bash
+
+	hpcf_interactive
+
+    module load python/2.7.13
+
+    run_lsf.py -f fastq.tsv -p leafcutter -g hg19 --design_matrix $PWD/design.tsv
+
+Output
+^^^^^^
+
+Results are stored in the $jid folder. 
+
+