---
title: "BEDtools"
author: "Celeste Valdivia"
date: "2023-05-18"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Curling in the bed file with gene information.
```{r, engine='bash'}
cd ../data 
curl -O https://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_genes.bed
```

Converting the bam file to bed
```{r, engine='bash'}
/home/shared/bedtools2/bin/bedtools bamtobed -i ../data/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam > ../output/08-19F.bed
```
Getting coverage of sequence reads:
```{r, engine='bash'}
/home/shared/bedtools2/bin/bedtools coverage \
-a ../data/C_virginica-3.0_Gnomon_genes.bed \
-b ../output/08-19F.bed \
> ../output/08-gene-19F-coverage.out
```

Curling bed files of transposable elements and lncRNA:
```{r, engine='bash', eval=F}
cd ../data
curl -O http://owl.fish.washington.edu/halfshell/genomic-databank/cgigas_uk_roslin_v1_gene.gff 
curl -O http://owl.fish.washington.edu/halfshell/genomic-databank/cgigas_uk_roslin_v1_rm.te.bed 
curl -O http://owl.fish.washington.edu/halfshell/genomic-databank/cgigas_uk_roslin_v1_lncRNA.gff
```
Intersect command in bedtools:
```{r, engine='bash'}
/home/shared/bedtools2/bin/bedtools intersect \
-a ../data/cgigas_uk_roslin_v1_gene.gff \
-b ../data/cgigas_uk_roslin_v1_rm.te.bed \
> ../output/08-gene-TE-intersect.out

head -2 ../output/08-gene-TE-intersect.out
```
Closest command in bedtools:
```{r, engine='bash'}
/home/shared/bedtools2/bin/bedtools closest \
-a ../data/cgigas_uk_roslin_v1_lncRNA.gff \
-b ../data/cgigas_uk_roslin_v1_gene.gff \
> ../output/08-lnc-gene-closet.out
```