Hello, I have custom tracks with my ChIP-seq data on the UCSC browser. I created the bigWig files from the BAM files using deepTools' bamCoverage.
I explored my files in IGV, IGB and UCSC browser. I would like to stick to the third one because has other nice functionalities, but I can´t seem to find the way of zooming out to a genome wide view as I can do with the other two tools. I keep pressing zoom out x100 but it´s still stuck in chromosome 8 showing me the same region, as if it couldn´t go further than that. (the coordinate I am at is: chr8:1-146,364,022 146,364,022 bp). There is a nice trend across the conditions that I would like to visualize genome-wide.
I wondered if this is possible or not. Also, is there a faster way than pressing zoom out x100 all the time until eventually reaching?
(genome: hg19, bamCoverage parameters: -bs 20 --normalizeUsing RPGC --effectiveGenomeSize 2685511504 , I chose that effective genome size because I did MAPQ filtering of reads, so I used the one of the second table that says "use in case you do multimapped reads filtering". Read length 50bp, single-end).
2) Another question: if I did differential binding analysis and normalized using the TMM method (DiffBind package in R), my bigwigs should be also generated with the same normalization, or it´s ok that I chose RPGC? Even though these are not concatenated steps, should I be consistent with the normalization method? or for this particular purpose it´s ok?