convert bam file to bedgraph format with inconsistent results

[zhiqiang]

Hi, all

I was trying to convert a sam/bam file into bedgraph files using two different approaches, and found that the results are different:

way 1: I used the program 'wiggles' shipped with tophat 1.3.2:

 samtools view part1.bam > part1.sam
 wiggles part1.sam part1.wiggles.bedgraph

way 2: I used the genomeCoverageBed from bedtools v2.16.2:

        samtools sort part1.bam part1.sorted
        genomeCoverageBed -bga -ibam part1.sorted.bam -g  chrom.sizes > part1.bedtool.bedgraph

In the result files, part1.wiggles.bedgraph and part1.bedtool.bedgraph were different in many genomic regions.

Have anyone experienced with this? it's really confusing.

one of the differences was like this:
1 3927 3931 6 | 1 3927 3930 6
1 3931 3935 5 | 1 3930 3931 2
1 3935 4092 4 | 1 3931 3935 1