I’m new to Chip-Seq data analysis and I’m using the Biostar handbook as reference which I find very useful. I understand that once I have the indexed bam file I can load it on IGV for peak detection but I can also use a smaller bed graph file to display coverages over intervals.
I used this command to create a bedgraph file but when I load it into IGV does not show any peak unlike the relative bam file
bedtools genomecov -ibam /SRR3033154_1.bam -g REF/saccer3.fa.fai -bg > SRR3033154_1.bedgraph
I wonder what it could be wrong since I followed the book tutorial step by step (I think..)