---
title: "IntersectBed"
author: "SR Code"
date: "3/18/2022"
output: html_document
---
```{bash}
#figure out where you are
pwd

```
```{bash}
#
cd ../data

wget --no-check-certificate http://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_mRNA.gff3

```
```{bash}

```

```{bash}
cd ../data
wget --no-check-certificate https://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_genes.bed
```

```{bash}
/home/shared/bedtools2/bin/bedtools intersect \
-a ../analysis/oilexp_dml.bed \
-b ../data/C_virginica-3.0_Gnomon_mRNA.gff3 \
-wb | head

```

```{bash}

/home/shared/bedtools2/bin/bedtools intersect \
-a ../analysis/oilexp_dml.bed \
-b ../data/C_virginica-3.0_Gnomon_genes.bed \
-wb | head

```
```{bash}

/home/shared/bedtools2/bin/bedtools intersect \
-a ../analysis/oilexp_dml.bed \
-b ../data/C_virginica-3.0_Gnomon_genes.bed \
-wb \
> ../analysis/dmlIntersectGenes.txt

```
