more on tracks

.vscode/settings.json

@@ -1,3 +1,3 @@
 {
-    "restructuredtext.confPath": "/Users/dli/eg-docs/docs"
+    "restructuredtext.confPath": "c:\\Users\\D\\web\\eg-docs\\docs"
 }

docs/tracks.rst

@@ -1,14 +1,41 @@
 Tracks
 ======
 
-This following sections introduce the track types the browser supports.
+.. important:: since all tracks are hosted on the web with HTTP/HTTPS links provided
+               for submitting as tracks, the webservers which are hosting the track
+               files need enable Cross-Origin Resource Sharing (CORS).
+
+
+Quoted from MDN_::
+
+    Cross-Origin Resource Sharing (CORS) is a mechanism that uses additional 
+    HTTP headers to tell a browser to let a web application running at 
+    one origin (domain) have permission to access selected resources 
+    from a server at a different origin. A web application makes a 
+    cross-origin HTTP request when it requests a resource that has 
+    a different origin (domain, protocol, and port) than its own origin.
+
+.. _MDN: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
+
+Configure your webserver to enable CORS
+---------------------------------------
+
+Most likely the browser domain is different with the server the tracks are hosted, the hosting server
+need enable CORS, for Apache web server in Ubuntu, this setup would work::
+
+    Header always set Access-Control-Allow-Origin "*"
+    Header always set Access-Control-Allow-Methods "POST, GET, OPTIONS, DELETE, PUT"
+    Header always set Access-Control-Max-Age "1000"
+    Header always set Access-Control-Allow-Headers "x-requested-with, Content-Type, origin, authorization, accept, client-security-token"
+
 
 Prepare track files
 -------------------
 
 The browser access the track files from its URL, only the proportion of the data in
-the specific viewed region are transferred to the browser for visualization. Thur, all
-the track files need be hosted in a web accssible location use HTTP or HTTPS.
+the specific viewed region are transferred to the browser for visualization. Thus, all
+the track files need be hosted in a web accssible location use HTTP or HTTPS. 
+The following sections introduce the track types the browser supports.
 
 Binary track file format like bigWig_ and HiC_ can be used directly with the browser.
 bedGraph_, methylC_ and categorical_ track files need 
@@ -18,15 +45,14 @@ at the same URL with the ``.gz`` file.
 
 Bed like format track files need be sorted first, say we have a track file named ``track.bedgraph``,
 we can use generic Linux ``sort`` command or the ``bedSort`` tool from UCSC. The following 2 commands
-do the same thing.
-
-    sort -k1,1 -k2,2n track.bedgraph > track.bedgraph.sorted
-
-or
+do the same thing::
 
+    # use Linux sort
+    sort -k1,1 -k2,2n track.bedgraph > track.bedgraph.sorted 
+    # or using bedSort
     bedSort track.bedgraph track.bedgraph.sorted
 
-then compressed and index using tabix:
+then compressed and index using tabix::
 
     bgzip track.bedgraph.sorted
     tabix -p bed track.bedgraph.sorted.gz
@@ -36,28 +62,6 @@ The two files must be in the same directory. Obtain the URL to "track.bedgraph.s
 
 .. _`compressed by bgzip and indexed by tabix`: http://www.htslib.org/doc/tabix.html
 
-Configure your webserver to enable CORS
----------------------------------------
-
-Quoted from MDN_:
-
-    Cross-Origin Resource Sharing (CORS) is a mechanism that uses additional HTTP headers
-    to tell a browser to let a web application running at one origin (domain) 
-    have permission to access selected resources from a server at a different origin. 
-    A web application makes a cross-origin HTTP request when it requests a resource that
-    has a different origin (domain, protocol, and port) than its own origin.
-
-.. _MDN: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
-
-Since the browser domain is different with the server the tracks are hosted, the hosting server
-need enable CORS, for Apache web server in Ubuntu, this setup would work:
-
-    Header always set Access-Control-Allow-Origin "*"
-    Header always set Access-Control-Allow-Methods "POST, GET, OPTIONS, DELETE, PUT"
-    Header always set Access-Control-Max-Age "1000"
-    Header always set Access-Control-Allow-Headers "x-requested-with, Content-Type, origin, authorization, accept, client-security-token"
-
-
 Numerical Tracks
 ----------------
 
@@ -74,7 +78,6 @@ Please check `UCSC bigWig`_ page to learn more about this format.
 
 .. _UCSC bigWig: https://genome.ucsc.edu/goldenpath/help/bigWig.html
 
-
 bedGraph
 ~~~~~~~~
 
@@ -100,20 +103,54 @@ left to right are ``chromosome``, ``start position`` (0-based), ``end position``
 Methylation tracks
 ------------------
 
+Methylation experiment like MeDIP-seq or MRE-seq can use `bigWig`_ or `bedGraph`_ format.
+For WGBS if users want to show read depth, methylation context along with methylation
+level, we usually format the data to `methylC`_ format, described below.
+
 methylC
 ~~~~~~~
 
-Methylation data are formatted in ``methylC`` format, which is a 7 column bed format file.
+Methylation data are formatted in ``methylC`` format, which is a 7 column bed format file::
+
+    chr1    10542   10543   CG      0.923   -       26
+    chr1    10556   10557   CHH     0.040   -       25
+    chr1    10562   10563   CG      0.941   +       17
+    chr1    10563   10564   CG      0.958   -       24
+    chr1    10564   10565   CHG     0.056   +       18
+    chr1    10566   10567   CHG     0.045   -       22
+    chr1    10570   10571   CG      0.870   +       23
+    chr1    10571   10572   CG      0.913   -       23
+
+Each line contains 7 fields separated by Tab. The fields are 
+``chromosome``, ``start position`` (0-based), ``end position`` (not included),
+``methylation context`` (CG, CHG, CHG etc.), ``methylation value``, ``strand``
+and ``read depth``.
 
 Categorical tracks
 ------------------
 
+Categorical tracks represents genomic bins for different categories. The most popular
+case is to represent chromHMM data, say which region is like enhancer, which region is
+likey promoter etc.
+
 categorical
 ~~~~~~~~~~~
 
+Example lines for ``categorical`` track are almost same as `bedGraph`_, the difference is 
+4th column is the category type, can use string or number here::
+
+    chr1    start1  end1    category1
+    chr2    start2  end2    category2
+    chr3    start3  end3    category3
+    chr4    start4  end4    category4
+
 Long range chromatin interaction
 --------------------------------
 
+Long range chromatin interaction data are used to show relatioships from diffenent
+genomic regions. `HiC`_ is used very often to show the result from a HiC experiment.
+
 HiC
 ~~~
 
+Learn more about HiC format please check https://github.com/aidenlab/juicer/wiki/Data.