Entering edit mode
7.9 years ago
Shicheng Guo
★
9.4k
Hi All,
What happened? wigToBigWig said "Where in.wig is in one of the ascii wiggle formats, but not including track lines", However, I found you can take wig.gz as the input, also, It is okay even you have track header in the fist line of wig?
Everything is Right?
Thanks.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
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.cse.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.
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
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.