2024-10-19 bed转换为bw文件

#!usr/bin/bash

# Input and output file paths
INPUT_BED="outs/reads.bed.gz"
OUTPUT_BIGWIG="outs/reads.bw"
CHROM_SIZES="genome.sizes"

# Temporary files
TEMP_BEDGRAPH="temp.bedgraph"

# Check if required tools are installed
command -v bedtools >/dev/null 2>&1 || { echo >&2 "bedtools is required but not installed. Aborting."; exit 1; }
command -v bedGraphToBigWig >/dev/null 2>&1 || { echo >&2 "bedGraphToBigWig is required but not installed. Aborting."; exit 1; }

# Step 1: Convert BED to bedGraph
echo "Converting BED to bedGraph..."
zcat "$INPUT_BED" | bedtools genomecov -bg -i stdin -g "$CHROM_SIZES" > "$TEMP_BEDGRAPH"

# Step 2: Sort the bedGraph file
echo "Sorting bedGraph..."
LC_COLLATE=C sort -k1,1 -k2,2n "$TEMP_BEDGRAPH" -o "$TEMP_BEDGRAPH"

# Step 3: Convert bedGraph to bigWig
echo "Converting bedGraph to bigWig..."
bedGraphToBigWig "$TEMP_BEDGRAPH" "$CHROM_SIZES" "$OUTPUT_BIGWIG"

# Clean up temporary files
rm "$TEMP_BEDGRAPH"

echo "Conversion complete. BigWig file created at $OUTPUT_BIGWIG"