Commit ef523fc2 authored by Michael Menzel's avatar Michael Menzel

updated readme

parent 35d3eedd
# Enhort: Genomic Position Profiling
The rise of high-throughput methods in genomic research greatly expanded our knowledge about the functionality of the genome. At the same time, the amount of available genomic position data increased massively, e.g., through genome-wide profiling of protein binding, virus integration or DNA methylation. However, there is no specialized software to investigate integration site profiles of virus integration or transcription factor binding sites by correlating the sites with the diversity of available genomic annotations.
The rise of high-throughput methods in genomic research greatly expanded our
knowledge about the functionality of the genome. At the same time, the amount
of available genomic position data increased massively, e.g., through genome-wide
profiling of protein binding, virus integration or DNA methylation.
However, there is no specialized software to investigate integration site profiles
of virus integration or transcription factor binding sites by correlating the sites
with the diversity of available genomic annotations.
Here we present Enhort, a user-friendly software tool for relating large sets of genomic positions to a variety of annotations. It functions as a statistics based genome browser, not focused on a single locus but analyzing many genomic positions simultaneously. Enhort provides comprehensive yet easy-to-use methods for statistical analysis, visualization, and the adjustment of background models according to experimental conditions and scientific questions.
Here we present Enhort, a user-friendly software tool for relating large sets of
genomic positions to a variety of annotations. It functions as a statistics based
genome browser, not focused on a single locus but analyzing many genomic positions
simultaneously. Enhort provides comprehensive yet easy-to-use methods for statistical
analysis, visualization, and the adjustment of background models according to
experimental conditions and scientific questions.
......@@ -13,7 +24,7 @@ Enhort is publicly available online at www.enhort.mni.thm.de and published under
# Build
Enhort is build using Maven. Some tests do not work well using mvn, the build is possible by skipping the test with -DskipTests=true
Enhort is build using Maven. Some tests do not work well using mvn and need some files to be set up to work, the build is possible by skipping the test with -DskipTests=true
Enhort works using a backend server and a frontend webserver. Both need to be build and deployed. Additionally Enhort needs a sqlite database for all annotations and a directory containing the .bed files. The current database is uploaded as example.db
......@@ -23,7 +34,8 @@ The connection ip to connect the Frontend to backend needs to be changed in the
The backend needs the used genomes as .fa files. The directory needs to be given upon start of the backend as parameter. Example call:
/usr/bin/java -jar -Xmx60g -XX:StringTableSize=1000003
```/usr/bin/java -jar -Xmx60g -XX:StringTableSize=1000003
enhort.jar
data/dir
example.db
```
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......
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