Is there a out of the box to convert a .bam file to a .wig file at specific resolution/bin size?
I was thinking to use igvtools, but I am not sure how it works:
igvtools count -z 5 -w 25 -e 250 alignments.bam alignments.cov.tdf hg19
What is the diffrence between
-z num Specifies the maximum zoom level to precompute. The default value is 7 and is sufficient for most files. To reduce file size at the expense of IGV performance this value can be reduced. -e, --extFactor num The read or feature is extended by the specified distance in bp prior to counting. This option is useful for chip-seq and rna-seq applications. The value is generally set to the average fragment length of the library minus the average read length. -w, --windowSize num The window size over which coverage is averaged. Defaults to 25 bp.