bedToBigBed manual with usage examples

bedToBigBed in.bed chrom.sizes out.bb

This tool is part of UCSC Genome Browser's utilities.

in.bed: file in one of the ascii bed formats, but not including track lines. The file must be sorted by chromosome and start. To sort a bed file, use the unix sort command:
```
sort -k1,1 -k2,2n unsorted.bed > sorted.bed
```
chrom.sizes: Chromosome size file. The file should tab delimited and structured as follows: <chromName> <chromSize>. You can get this file for the genome release that you are working with by using fetchChromSizes. Do not make up a chrom sizes from your own information.
out.bb: is the output indexed big bed file.

-type=bedN[+[P]] :
- N is between 3 and 15
- optional (+) if extra "bedPlus" fields,
- optional P specifies the number of extra fields. Not required, but preferred.
- Examples: -type=bed6 or -type=bed6+ or -type=bed6+3
-as=fields.as: If you have non-standard "bedPlus" fields, it's great to put a definition of each field in a row in AutoSql format here.
-blockSize=N: Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N: Number of data points bundled at lowest level. Default 512.
-unc: If set, do not use compression.
-tab: If set, expect fields to be tab separated, normally expects white space separator.
-extraIndex=fieldList: If set, make an index on each field in a comma separated list. -extraIndex=name and -extraIndex=name,id are commonly used.

bedToBigBed