bedGraphToBigWig Tutorial and Report

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations. 

1, bedGraph should be without header before sorting

awk 'NR!=1' input.bedGraph > input.deheader.bedGraph

2, bedGraph should be sorted

  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph

3, chorsome length should be same with Bam files

 fetchChromSizes hg19 > hg19.chrom.sizes

​4, Be sure the bedGraph should only have 4 column 

awk '{print $1,$2,$3,$4}' NC-P-2.bedGraph_CpG.sort.bedGraph > NC-P-2.bedGraph_CpG.sort.4.bedGraph

5, Now, you can run the script (bedGraphToBigWig input.sort.bam chrome.size


Summary, You can use the following two step to do bedGraphtobigwig transformation:

(head -n 1 NC-P-25.bedGraph_CpG.bedGraph && tail -n +2 NC-P-25.bedGraph_CpG.bedGraph | sort -k1,1 -k2,2n | awk '{print $1,$2,$3,$4}' OFS="t" )  > NC-P-25.bedGraph_CpG.bedGraph.sort

bedGraphToBigWig NC-P-25.bedGraph_CpG.bedGraph.sort  hg19.chrom.sizes

For large number of bedGraph files:

# bedgraph to bigwig
for i in `ls *bedGraph`
(head -n 1 $i && tail -n +2 $i | sort -k1,1 -k2,2n | awk '{print $1,$2,$3,$4}' OFS="t" )  > $i.sort
bedGraphToBigWig $i.sort ~/oasis/db/hg19/hg19.chrom.sizes $ 


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