---
title: "16-miRNA vis"
author: "Steven Roberts"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
editor_options: 
  markdown: 
    wrap: sentence
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```


Apul

# Genome 

https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/data/GCF_013753865.1_Amil_v2.1_genomic.fna


Get stuff from NCBI

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_013753865.1/

```{bash}
/home/shared/datasets download genome accession GCF_013753865.1 --include gff3,gtf,gbff
```

```{bash}

unzip ../data/ncbi_dataset.zip
```




# short stack

/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out

See: https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/

```{r, engine='bash', eval=TRUE}
head ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
```

```{r, engine='bash', eval=TRUE}
wc -l ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
```
```{r, engine='bash', eval=TRUE}
grep -c ">" ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
```


# IGV 

![igv](https://gannet.fish.washington.edu/seashell/snaps/IGV_2024-05-16_09-56-45.png)

IGV session file: https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/code/16.1.ivg_session.xml


```
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Session genome="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/data/GCF_013753865.1_Amil_v2.1_genomic.fna" hasGeneTrack="false" hasSequenceTrack="true" locus="NC_058068.1:0-19500522" version="8">
    <Resources>
        <Resource path="https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.bed" type="bed"/>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3" type="gff3"/>
        <Resource path="http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.gff" type="gff"/>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3" type="gff3"/>
    </Resources>
    <Panel height="792" name="FeaturePanel" width="1752">
        <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="false" visible="true"/>
        <Track attributeKey="GCF_013753865.1_Amil_v2.1_genomic.gff" clazz="org.broad.igv.track.FeatureTrack" displayMode="EXPANDED" fontSize="20" groupByStrand="false" height="100" id="http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.gff" name="GCF_013753865.1_Amil_v2.1_genomic.gff" visible="true"/>
        <Track attributeKey="Results.gff3" clazz="org.broad.igv.track.FeatureTrack" colorScale="ContinuousColorScale;0.0;69.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="20" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3" name="Results.gff3" visible="true"/>
        <Track attributeKey="known_miRNAs.gff3" clazz="org.broad.igv.track.FeatureTrack" fontSize="20" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3" name="known_miRNAs.gff3" visible="true"/>
        <Track attributeKey="Apul_lncRNA.bed" clazz="org.broad.igv.track.FeatureTrack" fontSize="20" groupByStrand="false" id="https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.bed" name="Apul_lncRNA.bed" visible="true"/>
    </Panel>
    <PanelLayout dividerFractions="0.007471980074719801"/>
    <HiddenAttributes>
        <Attribute name="DATA FILE"/>
        <Attribute name="DATA TYPE"/>
        <Attribute name="NAME"/>
    </HiddenAttributes>
</Session>
```