有用的UCSC tools推荐

先上网站链接，这些都不需要安装，直接下载下来就可以用，比较便捷
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

1. bedGeneParts - Given a bed, spit out promoter, first exon, or all introns.

bedGeneParts part in.bed out.bed
Where part is either 'exons' or 'firstExon' or 'introns' or 'promoter' or 'firstCodingSplice' or 'secondCodingSplice'
options:
   -proStart=NN - start of promoter relative to txStart, default -100
   -proEnd=NN - end of promoter relative to txStart, default 50

2. bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.

bedGraphToBigWig in.bedGraph chrom.sizes out.bw
where in.bedGraph is a four column file in the format:
      <chrom> <start> <end> <value>
and chrom.sizes is a two-column file/URL: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like
  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes
or you may use the script fetchChromSizes to download the chrom.sizes file.
If not hosted by UCSC, a chrom.sizes file can be generated by running
twoBitInfo on the assembly .2bit file.
The input bedGraph file must be sorted, use the unix sort command:
  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph
options:
   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -unc - If set, do not use compression.

3. bigWigAverageOverBed v2 - Compute average score of big wig over each bed, which may have introns.

bigWigAverageOverBed in.bw in.bed out.tab
The output columns are:
   name - name field from bed, which should be unique
   size - size of bed (sum of exon sizes
   covered - # bases within exons covered by bigWig
   sum - sum of values over all bases covered
   mean0 - average over bases with non-covered bases counting as zeroes
   mean - average over just covered bases
Options:
   -stats=stats.ra - Output a collection of overall statistics to stat.ra file
   -bedOut=out.bed - Make output bed that is echo of input bed but with mean column appended
   -sampleAroundCenter=N - Take sample at region N bases wide centered around bed item, rather
                     than the usual sample in the bed item.
   -minMax - include two additional columns containing the min and max observed in the area.

4. bigWigCorrelate - Correlate bigWig files, optionally only on target regions.

bigWigCorrelate a.bigWig b.bigWig
or
   bigWigCorrelate listOfFiles
options:
   -restrict=restrict.bigBed - restrict correlation to parts covered by this file
   -threshold=N.N - clip values to this threshold
   -rootNames - if set just report the root (minus directory and suffix) of file
                names when using listOfFiles
   -ignoreMissing - if set do not correlate where either side is missing data
                Normally missing data is treated as zeros

5. bigWigMerge v2 - Merge together multiple bigWigs into a single output bedGraph.

You'll have to run bedGraphToBigWig to make the output bigWig.
The signal values are just added together to merge them

bigWigMerge in1.bw in2.bw .. inN.bw out.bedGraph
options:
   -threshold=0.N - don't output values at or below this threshold. Default is 0.0
   -adjust=0.N - add adjustment to each value
   -clip=NNN.N - values higher than this are clipped to this value
   -inList - input file are lists of file names of bigWigs
   -max - merged value is maximum from input files rather than sum

6. fetchChromSizes

fetchChromSizes <db> > <db>.chrom.sizes
    used to fetch chrom.sizes information from UCSC for the given <db>
<db> - name of UCSC database, e.g.: hg38, hg18, mm9, etc ...

This script expects to find one of the following commands:
    wget, mysql, or ftp in order to fetch information from UCSC.
Route the output to the file <db>.chrom.sizes as indicated above.
This data is available at the URL:
  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes

Example:   fetchChromSizes hg38 > hg38.chrom.sizes