#!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"
2024-10-19 bed转换为bw文件
最后编辑于 ：
©著作权归作者所有,转载或内容合作请联系作者
禁止转载，如需转载请通过简信或评论联系作者。
- 文/潘晓璐 我一进店门，熙熙楼的掌柜王于贵愁眉苦脸地迎上来，“玉大人，你说我怎么就摊上这事。” “怎么了？”我有些...
- 文/花漫 我一把揭开白布。 她就那样静静地躺着，像睡着了一般。 火红的嫁衣衬着肌肤如雪。 梳的纹丝不乱的头发上，一...
- 文/苍兰香墨 我猛地睁开眼，长吁一口气：“原来是场噩梦啊……” “哼！你这毒妇竟也来了？” 一声冷哼从身侧响起，我...
