951a2f1ae953b7f284a8865ba7c6810823142b61
gperez2
  Fri Apr 22 09:53:56 2022 -0700
Updating ReMap track images, refs #28960

diff --git src/hg/makeDb/trackDb/mouse/reMap.html src/hg/makeDb/trackDb/mouse/reMap.html
index 62b3c21..aa92845 100644
--- src/hg/makeDb/trackDb/mouse/reMap.html
+++ src/hg/makeDb/trackDb/mouse/reMap.html
@@ -3,34 +3,32 @@
 This track represents the <a href="http://remap.univ-amu.fr/"
 target="_blank">ReMap Atlas</a> of regulatory regions, which consists of a
 large-scale integrative analysis of all Public ChIP-seq data for transcriptional
 regulators from GEO, ArrayExpress, and ENCODE. 
 </p>
 
 <p>
 Below is a schematic diagram of the types of regulatory regions: 
 <ul>
 <li>ReMap 2022 Atlas (all peaks for each analyzed data set)</li> 
 <li>ReMap 2022 Non-redundant peaks (merged similar target)</li>
 <li>ReMap 2022 Cis Regulatory Modules</li>
 </ul>
 </p>
 
-<img src="http://remap.univ-amu.fr/storage/public/hubReMap2022/img/schema_datatype_remap.png"
-alt="Schematic diagram data types" style="display: block; margin-left: left;
-margin-right: auto; max-width:800px">
-<br>
+<img style='margin-left: 40px;' height=229 width=500
+src="../images/reMap_schema_datatype.png">
 
 <h2> Display Conventions and Configuration </h2>
 <ul>
 <li>
 Each transcription factor follows a specific RGB color.
 </li>
 <li>
 ChIP-seq peak summits are represented by vertical bars.
 </li>
 <li>
 Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given
 GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in
 a particular biological condition (e.g. MCF-7).
 <br>Data sets are labeled with the concatenation of these three pieces of
 information (e.g. GSE41561.ESR1.MCF-7).
@@ -51,33 +49,32 @@
 This release of ReMap (2022) presents the analysis of 5,505 quality controlled
 mouse ChIP-seq (n=7,317 before QCs) from public sources (GEO & ENCODE). Those
 ChIP-seq data sets have been mapped to the GRCm38/mm10 mouse assembly. The data
 set is defined as a ChIP-seq experiment in a given series (e.g. GSE122715),
 for a given TF (e.g. USF1), in a particular biological condition (i.e. cell
 line, tissue type, disease state, or experimental conditions; e.g. mESC).
 Data sets were labeled by concatenating these three pieces of information, such
 as GSE122715.USF1.mESC.
 </p>
 <p>Those merged analyses cover a total of 656 DNA-binding proteins
 (transcriptional regulators) such as a variety of transcription factors (TFs),
 transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for
 123 million peaks.
 </p>
 
-<img src="http://remap.univ-amu.fr/storage/public/hubReMap2022/img/Arhgap26_hgt_genome_euro_bc5a_b868b0.png"
-alt="Schematic diagram" style="display: block; margin-left: left; margin-right: auto; max-width:800px">
-<br>
+<img style='margin-left: 40px;' height=500 width=500
+src="../images/mouseReMap.png">
 
 <h4>ENCODE</h4>
 Available ENCODE ChIP-seq data sets for transcriptional regulators from the
 www.encodeproject.org portal were processed with the standardized ReMap pipeline.
 The list of ENCODE data was retrieved as FASTQ files from the ENCODE portal
 (https://www.encodeproject.org/) using filters. Metadata information in JSON
 format and FASTQ files were retrieved using the Python requests module.
 
 
 <h4>ChIP-seq processing</h4>
 Both Public and ENCODE data were processed similarly. Bowtie 2 (<a href=
 "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381/" TARGET =_BLANK
 >PMC3322381</a>) (version 2.2.9) with options -end-to-end -sensitive was used to align all
 reads on the human genome (GRCh38/hg38 assembly). Biological and technical
 replicates for each unique combination of GSE/TF/Cell type or Biological condition