Merge pull request #22 from arnavm/master

Rename CallingCard to QBed
lidaof · Apr 20, 2020 · 980814d · 980814d
2 parents 7f0db2e + 67a6f47
commit 980814d
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diff --git a/docs/datahub.rst b/docs/datahub.rst
@@ -268,14 +268,14 @@ Example genomealign track
         }
     }
 
-Example callingcard track
+Example qBED track
 -------------------------
 
 .. code-block:: json
 
     {
-        "type":"callingcard",
-        "url":"https://htcf.wustl.edu/files/RdNgrGeQ/HCT116-PBase.ccf.gz",
+        "type":"qbed",
+        "url":"https://htcf.wustl.edu/files/RdNgrGeQ/HCT116-PBase.qbed.gz",
         "name":"piggyBac insertions",
         "showOnHubLoad":"true",
         "options":{
@@ -289,9 +289,9 @@ Example callingcard track
           },
     }
 
-.. note:: Default callingcard track options are ``"logScale":"none"``, ``"show":"all"``, ``"markersize":3``, and ``"opacity":[100]``.
+.. note:: Default qBED track options are ``"logScale":"none"``, ``"show":"all"``, ``"markersize":3``, and ``"opacity":[100]``.
           Log-scaling can be set by specifying ``"logScale":"log10"``. To change opacity, pass a single value in brackets, as in the above example.
-          Calling card tracks will, by default, plot all entries in view. For information-dense regions, this can lead to excessive memory consumption.
+          qBED tracks will, by default, plot all entries in view. For information-dense regions, this can lead to excessive memory consumption.
           To plot a random subsample instead, specify ``"show":"sample"`` and pass the number of points to visualize to ``"sampleSize"``, e.g.
           ``"sampleSize":1000``
 
@@ -376,7 +376,7 @@ type
 * genomealign
 * longrange
 * bigInteract
-* callingcard
+* qBED
 * matplot
 * snp
 * ruler

diff --git a/docs/tracks.rst b/docs/tracks.rst
@@ -388,10 +388,10 @@ Thanks to the higlass team who provides the data API, the browser is able to dis
 from the higlass server, for example, you can use the uuid ``Hyc3TZevQVm3FcTAZShLQg`` to represent the track for *Aiden et al. (2009) GM06900 HINDIII 1kb*,
 for a full list of available cool tracks please check http://higlass.io/api/v1/tilesets/?dt=matrix
 
-Calling card track
+qBED track
 ------------------
 
-Calling Card Format (CCF) is tab-delimited, plain text format for discrete genomic data, such as transposon insertions. This format requires a minimum of four columns and supports up to six. The four required columns are CHROM, START, END, and VALUE, where VALUE is a numeric value (i.e. an int or float). As with BED files, the START and END coordinates are 0-indexed. The fifth and sixth columns are optional and represent STRAND and ANNOTATION, respectively. The ANNOTATION column can be used to store sample- or entry- specific information, such as a replicate barcode. Here is an example of a four-column CCF file::
+qBED is tab-delimited, plain text format for discrete genomic data, such as transposon insertions. This format requires a minimum of four columns and supports up to six. The four required columns are CHROM, START, END, and VALUE, where VALUE is a numeric value (i.e. an int or float). As with BED files, the START and END coordinates are 0-indexed. The fifth and sixth columns are optional and represent STRAND and ANNOTATION, respectively. The ANNOTATION column can be used to store sample- or entry- specific information, such as a replicate barcode. Here is an example of a four-column qBED file::
 
     chr1    41954321        41954325        1
     chr1    41954321        41954325        18
@@ -405,7 +405,7 @@ Calling Card Format (CCF) is tab-delimited, plain text format for discrete genom
     chr1    54747055        54747059        4
     chr1    60748489        60748493        2
 
-Here is an example of a six-column CCF file::
+Here is an example of a six-column qBED file::
 
     chr1    51441754        51441758        1       -       CTAGAGACTGGC
     chr1    51441754        51441758        21      -       CTTTCCTCCCCA
@@ -418,15 +418,15 @@ Here is an example of a six-column CCF file::
     chr1    61106283        61106287        7       -       CGTTTTTCACCT
     chr1    61542006        61542010        1       -       CTGAGAGACTGG
 
-Your text file must be sorted by the first three columns. If your filename is example.ccf, you can sort it with the following command: ``sort -k1V -k2n -k3n example.ccf > example_sorted.ccf``
-Alternatively, with ``bedops``: ``sort-bed example.ccf > example_sorted.ccf``
+Your text file must be sorted by the first three columns. If your filename is example.qbed, you can sort it with the following command: ``sort -k1V -k2n -k3n example.qbed > example_sorted.qbed``
+Alternatively, with ``bedops``: ``sort-bed example.qbed > example_sorted.qbed``
 
 Note that you can have strand information without a barcode, but you cannot have barcode information without a strand column.
 
-Place your sorted CCF file in a web-accessible directory, then compress and index as follows::
+Place your sorted qBED file in a web-accessible directory, then compress and index as follows::
 
-    bgzip example_sorted.ccf
-    tabix -p bed example_sorted.ccf.gz
+    bgzip example_sorted.qbed
+    tabix -p bed example_sorted.qbed.gz
 
 Matplot track
 -------------