---
title: "Bedtools"
output: html_document
---

```{bash}
cd ../genome-features
curl --insecure -O https://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_mRNA.gff3




```






```{bash}
cd ..
head igv/DET_sex_filtered_p-0.05_q-0.05.bed
head igv/sex_dml.bed 
```

```{bash}
head /Users/sr320/Desktop/2019-04-05-DML-Destrand-5x-Locations.bed
```




```{bash}
cd ..
/home/shared/bedtools2/bin/intersectBed \
-wb \
-a igv/oao_dml.bed \
-b genome-features/C_virginica-3.0_Gnomon_mRNA.gff3 \
| head

```


```{bash}
cd ..
/home/shared/bedtools2/bin/intersectBed \
-wb \
-a igv/oao_dml.bed \
-b genome-features/C_virginica-3.0_Gnomon_mRNA_yrv.gff3 

```







```{bash}
/Applications/bedtools2/bin/intersectBed \
-a igv/oao_dml.bed \
-b igv/sex_dml_02.bed \
| head

```