2022-11-14 bigwig文件转换为bed文件

在数据分析的时候经常碰到各种文件格式的相互转换，UCSC提供了一些工具。
去Anaconda工具库中搜索ucsc也出来很多的工具

有些人先将bigwig转换为wig，再将wig转换为bed

conda install -c bioconda ucsc-bigwigtowig
bigWigToWig signal.bigWig signal.wig

conda install -c bioconda bedops
 wig2bed < signal.wig > signal.bed

#Filter BED by its score column with `awk`:
awk '($5 < 1)' signal.bed > signal.filtered.bed

另外还有convert2bed工具

convert2bed -i wig -o bed --max-mem=8G  --sort-tmpdir=./ -x  < sample.wig  >sample.bed
注意：其中< 读取文件， >输出文件中的"<" 和 ">"必须要加，我没加一直报错~~
 
另外还有可能提示：
Warning: WIG data contains 0-indexed element at line 2
                Consider adding --zero-indexed (-x) option to convert zero-indexed WIG data
Warning: If your Wiggle data is a significant portion of available system memory, 
                use the --max-mem and --sort-tmpdir options, 
                or use --do-not-sort to disable post- 
                 conversion sorting. See --help for more information.

  Usage:  $ convert2bed --input=fmt [--output=fmt] [options] < input > output
 
 Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF
  and WIG genomic formats to BED or BEDOPS Starch (compressed BED)

  Input can be a regular file or standard input piped in using the
  hyphen character ('-'):

  $ some_upstream_process ... | convert2bed --input=fmt - > output

  Input (required):

  --input=[bam|gff|gtf|gvf|psl|rmsk|sam|vcf|wig] (-i )
      Genomic format of input file (required)

  Output:

  --output=[bed|starch] (-o )
      Format of output file, either BED or BEDOPS Starch (optional, default is BED)

  Other processing options:

  --do-not-sort (-d)
      Do not sort BED output with sort-bed (not compatible with --output=starch)
  --max-mem= (-m )
      Sets aside  memory for sorting BED output. For example,  can
      be 8G, 8000M or 8000000000 to specify 8 GB of memory (default is 2G)
  --sort-tmpdir= (-r )
      Optionally sets [dir] as temporary directory for sort data, when used in
      conjunction with --max-mem=[value], instead of the host's operating system
      default temporary directory
  --starch-bzip2 (-z)
      Used with --output=starch, the compressed output explicitly applies the bzip2
      algorithm to compress intermediate data (default is bzip2)
  --starch-gzip (-g)
      Used with --output=starch, the compressed output applies gzip compression on
      intermediate data
  --starch-note="xyz..." (-e "xyz...")
      Used with --output=starch, this adds a note to the Starch archive metadata
  --help | --help[-bam|-gff|-gtf|-gvf|-psl|-rmsk|-sam|-vcf|-wig] (-h | -h )
      Show general help message (or detailed help for a specified input format)
  --version (-w)
      Show application version

在这里我用的是 ucsc-bigwigtobedgraph

conda install -c bioconda ucsc-bigwigtobedgraph
bigWigToBedGraph in.bw out.bed

usage:
   bigWigToBedGraph in.bigWig out.bedGraph
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

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