I am using ucsc bigWigToWig conversion tool to get a wiggle format file.
However the output format I get is:
bedGraph section chr1:10458-717292
chr1 10458 10459 7.7
chr1 10459 10460 7.8
chr1 10460 10461 7.9
chr1 10461 10462 8
chr1 10462 10464 8.1
chr1 10464 10465 8.2
chr1 10465 10467 8.3
I tried redownloading the tool from ucsc, checking if this is not a file name issue with ./
I tried using another bigwig file from ENCODE, same issue.
Because using ucsc bigwig to bedgraph conversion tool, I get a proper bedgraph, I decided to go backwards.
I converted bedgraph to bigwig to wig, again same thing.
The only difference that this file has compared to a usual bedgraph file is the section part added that describes schema of the following sequences(line 1 of table scheme above). While for a wiggle file format, I expect a one chromosomal position per unit output without chromosome name: http://genome.ucsc.edu/goldenpath/help/wiggle.html
I even tried using an older version of the tool from ucsc, same issue.
Any help would be much appreciated.