ucscbrowser_mouse.Rmd

---
title: "Mouse NeoCortex Track Hub for UCSC Genome Browser"
---

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<!-- ### Count Data -->

<!-- ```{r echo=FALSE, include=FALSE} -->
<!-- knitr::opts_chunk$set(warning = FALSE, message = FALSE)  -->
<!-- library(DT) -->
<!-- library(knitr) -->
<!-- datax_rna <- read.table("files/rna_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- datax_atac <- read.table("files/atac_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- datax_cage <- read.table("files/cage_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- ``` -->

<!-- #### **RNA-Seq** -->

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<!-- ``` {r fig1, echo = FALSE, include=TRUE} -->
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<!-- #### **ATAC-Seq** -->

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<!-- #### **CAGE-Seq** -->

<!-- <div align="center"> -->
<!-- ``` {r fig3, echo = FALSE, include=TRUE} -->
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<!-- ``` -->
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<!-- ### Genome Browser -->

<!-- <div align="center"> -->
<!--   <iframe width='1850px' height='1000px' frameBorder='0' src='https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr18%3A15393391%2D15410982&hgsid=1402705023_aKIR7wgaDGxjpAodVTAk7KXf1wpp'> -->
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; This track hub was built by aggregated **scRNA-Seq**, **scATAC-Seq** and **CAGE-Seq** reads of the mouse neocortex. You can query for positions, isoforms and genes to browse sequencing reads and ATAC-Seq and CAGE-Seq peaks. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; In order to download nucleotide sequences, simply go to **View** -> **DNA** ->  **get DNA**. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; See the [DolphinNext](https://dnext.dolphinnext.com/index.php?np=3&id=265) run for querying genes of interests on an aggregated gene expression and peaks data table, integrated to this UCSC Track Hub. Click to **Report** -> **UCSC Genome Browser**. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Please wait until the UCSC Genome Browser is fully loaded!

<div align="center">
  <iframe width='1650px' height='1000px' frameBorder='0' src='https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr18%3A15393391%2D15410982&hgsid=1537661975_iXiaJ28aYWDv7maWuCls6WIhFXZj'>
    <p>Your browser does not support iframes</p>
  </iframe>
</div>