---
title: "14-intersectbed"
output: html_document
date: "2024-12-23"
---


```{bash}
head ../output/12-IGV/myDiff1055p.bedgraph
```



https://gannet.fish.washington.edu/seashell/bu-github/project-mytilus-methylation/output/12-IGV/ncRNA.gff
```{bash}
wget -r \
--no-directories --no-parent \
-P ../output/12-IGV/ \
-A "*gff" https://gannet.fish.washington.edu/seashell/bu-github/project-mytilus-methylation/output/12-IGV/
```

```{bash}
# Input files
BEDGRAPH="../output/12-IGV/myDiff1055p.bedgraph"
GFF_DIR="../output/12-IGV"

# Output directory for intersect results
OUTPUT_DIR="../output/14-intersectbed/"
mkdir -p $OUTPUT_DIR

# Loop through all GFF files in the directory
for GFF in $GFF_DIR/*.gff; do
    BASENAME=$(basename "$GFF" .gff)
    OUTPUT_FILE="$OUTPUT_DIR/${BASENAME}_intersect.bed"
    
    echo "Intersecting $BEDGRAPH with $GFF..."
    bedtools intersect \
    -wb \
    -a "$BEDGRAPH" \
    -b "$GFF" > "$OUTPUT_FILE"
    
    echo "Result saved to $OUTPUT_FILE"
done

echo "All intersections completed!"
```
```{bash}
bedtools intersect

```

```{bash}
intersectBed
```