Hello,
I have some wiggle files output from FindPeaks, and I would like to view these in IGV. IGV informs me that I should make .tdf files as they are large. igvtools gives an error when attempting this:
>igvtools tile infile outfile genome_file
Processing chromosome 3LHet Error: Data is not sorted @ 3LHet 268822 (last position = 365311 max ext factor = 0)
A grep 'Step' on the wig file shows it is unordered:
fixedStep chrom=3RHet start=72044 step=1 span=1
fixedStep chrom=3RHet start=184322 step=1 span=1
fixedStep chrom=3RHet start=1301403 step=1 span=1
fixedStep chrom=3RHet start=1769380 step=1 span=1
fixedStep chrom=3RHet start=71684 step=1 span=1
fixedStep chrom=3RHet start=2432197 step=1 span=1
fixedStep chrom=3RHet start=8494 step=1 span=1
fixedStep chrom=3RHet start=7767 step=1 span=1
fixedStep chrom=3RHet start=5727 step=1 span=1
fixedStep chrom=3RHet start=4292 step=1 span=1
fixedStep chrom=3RHet start=4372 step=1 span=1
fixedStep chrom=3RHet start=111 step=1 span=1
fixedStep chrom=3RHet start=81 step=1 span=1
fixedStep chrom=3RHet start=59 step=1 span=1
So I sorted the declaration lines and associated data chunks in the wig.gz file using a custom Python script, and things seem to have improved, but it still falls down:
fixedStep chrom=3RHet start=59 step=1 span=1
fixedStep chrom=3RHet start=81 step=1 span=1
fixedStep chrom=3RHet start=111 step=1 span=1
fixedStep chrom=3RHet start=4292 step=1 span=1
fixedStep chrom=3RHet start=4372 step=1 span=1
fixedStep chrom=3RHet start=5727 step=1 span=1
fixedStep chrom=3RHet start=7767 step=1 span=1
fixedStep chrom=3RHet start=8494 step=1 span=1
fixedStep chrom=3RHet start=71684 step=1 span=1
fixedStep chrom=3RHet start=72044 step=1 span=1
fixedStep chrom=3RHet start=184322 step=1 span=1
fixedStep chrom=3RHet start=1301403 step=1 span=1
fixedStep chrom=3RHet start=1769380 step=1 span=1
fixedStep chrom=3RHet start=2432197 step=1 span=1
>igvtools tile infile outfile genome_file
Processing chromosome 3RHet
.........10.0%
.........20.0%
..
.........190.0%
....Error: Data is not sorted @ 3RHet 80 (last position = 2517507 max ext factor = 0)
Any ideas?
Cheers,
Neil
