I have bed file data that was mapped with Bowtie 1 and the output of this was converted to bed files.
After having done my data analysis my lab need to upload the bed file data, in coverage format, to the UCSC genome browser i.e. the data are needed in 'bigWig' format.
So I went about converting the data from BED to bigWig as follows:
#bed to bedGraph bedtools genomecov -i test.bed -g /storage/projects/teif/mm9_generic_data/mm9.genome -bg > test.bedGraph head test.bedGraph chr1 3000389 3000399 1 chr1 3000399 3000425 2 chr1 3000425 3000435 1 chr1 3000937 3000973 2 #bedGraph to bigWig /usr/local/ucscutils/bedGraphToBigWig test.bedGraph /storage/projects/teif/mm9_generic_data/mm9.genome test.bw #convert bigwig to wig in order to check contents /usr/local/ucscutils/bigWigToWig test.bw test.wig head test.wig fixedStep chrom=chr1 start=3000390 step=1 span=1 1 1 1 1 1 1 1 1 1 1 2 2
I also did the same for nucleosomes. I don't know why but the resultant wig file was different to the above- see below:
bedtools genomecov -i nucleosomes.bed -g /storage/projects/teif/mm9_generic_data/mm9.genome -bg > nucleosomes.bedGraph head nucleosomes.bedGraph chr1 3000018 3000019 1 chr1 3000019 3000034 2 chr1 3000034 3000035 3 chr1 3000035 3000044 7 /usr/local/ucscutils/bedGraphToBigWig nucleosomes.bedGraph mm9_data/mm9.genome nucleosomes.bw head nucleosomes.bw /usr/local/ucscutils/bigWigToWig nucleosomes.bw nucleosomes.wig head nucleosomes.wig #bedGraph section chr1:3000018-3007577 chr1 3000018 3000019 1 chr1 3000019 3000034 2 chr1 3000034 3000035 3 chr1 3000035 3000044 7
However there's a problem with the submission of the bigWig files to UCSC genome browser:
Unrecognized format line 1 of file: generegulation.org/NGS/test.bw (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
As you can see from the content of all the above created files there is no 'Chr' in the place of 'chr'.... This error happens in both the case of both 'test.bw' and 'nucleosomes.bw'. I have googled this error and each time that someone has had this problem it does not seem to be the case that there is a problem with the capitalisation of 'chr'... See links below:
similar problem with a bigwig file: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/zWYFn6yQ4p0
Does anything about my data immediately stand out as obvious such that the data is not uploadable to UCSC?