wigToBigWig support wig.gz and allow track as the fist line?
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5.5 years ago
Shicheng Guo ★ 8.9k

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.
wigToBigWig • 1.9k views
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