Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]

Motivation The ENCODE data comes out, and luckily they provide both .bam file and .bigwig file. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool: BEDtools and other related tools. Result I'll first upload the difference between my-version and official version: Top to Bottom:

• Black: my-version-POSitive-strand.bigwig
• Blue: Official-version-POSitive-strand.bigwig
• Red: Official-version-REVerse-strand.bigwig
• Grey: my-version-REVerse-strand.bigwig

From the image, we will find my-version-data and official-version-data roughly share the same peaks, however, my-version-peaks are somehow masked by certain uniform noises. And it drives me crazy. Note that I know not all the bioinformatics works can be reproduces, but this issue dose not get involved with much algorithms, decisions, etc. Therefore, it's supposed to be reproducible, I think. Data Set ENCODE/CSHL long RNA-seq Data set can be found here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/ And here I use K562-chromatin-subcellular fraction (Rep4) to explore as an example:

• BAM ...