two way get analysis data to get the obvious range difference in IGV

Question

[mikysyc2016]

Hi all, I do ChIP-seq for TF. And here I get tdf file through two different way. The up one i use bowtie2 and macs2 to analysis fastq file and get bedgraph file then use igvtool transfer to tdf file(the range from 0 -200). the bottom one I use whole homer analysis to get. The peak location look like same, but the peak range has big difference(the range form 0 -100). Did some know which one should be the right one ? And why this range different can happen? Thanks in adavance.

[mikysyc2016]

[GenoMax]

You can't attach images by pointing to a file on your desktop. You need to do it like this: How to add images to a Biostars post

[mikysyc2016]

Thanks! Can you see the picture now? I can not see the link by myself.

[mikysyc2016]

do not know how to upload the figure in my computer

[mikysyc2016]

[GenoMax]

You don't seem to be doing this right.

Here is one version I see: https://preview.ibb.co/ciMgfJ/q.jpg

[mikysyc2016]

Right! Thank you for your help!

Answer 1

[ATpoint]

Different tools, different outputs, mainly because (probably) some default parameters cause different behaviours. I recommend the latest version of deeptools bamCoverage to have things nice and reproducible:

bamCoverage -bs 1 --normalizeUsing CPM --bam in.bam -o file_CPM.bigwig -e <int>

This will give you a high-resolution browser track at base-pair resolution (-bs 1, the lower the bin size the smoother the peaks will look, but the program runs longer and files are bigger), normalized to the count per million (CPM). You can optionally and an integer value to -e to elongate the short reads to the average fragment size (if you have that information, based on gel or Bioanalyzer).