博文
如何将多个Bed文件进行合并？
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| 假如有1.bed, 2.bed, 3.bed,如何对这三个bed文件进行合并，去掉冗余的条目，得到一个并集all.bed？ 答案是bedtools的mergeBed [noncode@gnode105 script]$ mergeBed -h Tool: bedtools merge (aka mergeBed) Version: v2.16.2 Summary: Merges overlapping BED/GFF/VCF entries into a single interval. Usage: bedtools merge [OPTIONS] -i <bed/gff/vcf> Options: -s Force strandedness. That is, only merge features that are the same strand. - By default, merging is done without respect to strand. -n Report the number of BED entries that were merged. - Note: "1" is reported if no merging occurred. -d Maximum distance between features allowed for features to be merged. - Def. 0. That is, overlapping & book-ended features are merged. - (INTEGER) -nms Report the names of the merged features separated by semicolons. -scores Report the scores of the merged features. Specify one of the following options for reporting scores: sum, min, max, mean, median, mode, antimode, collapse (i.e., print a semicolon-separated list), - (INTEGER) Notes: (1) All output, regardless of input type (e.g., GFF or VCF) will in BED format with zero-based starts (2) The input file (-i) file must be sorted by chrom, then start.[/mw_shl_code] |
https://blog.sciencenet.cn/blog-1509670-847318.html
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