https://bioinformaticsonline.com/answers/view/23993/in-search-of-a-good-genome-browserviewer? https://bioinformaticsonline.com/answers/view/23993/in-search-of-a-good-genome-browserviewer Sat, 22 Aug 2015 10:31:44 -0500 https://bioinformaticsonline.com/answers/view/23993/in-search-of-a-good-genome-browserviewer I have reference sequeces (in fasta format) and alignment files (small RNA reads from 4 different conditions aligned to genome in SAM/BAM/BED/BEDgraph format) as input files. I'm interested in comaparing the alignments of different conditions. So, I'm looking for a good genome viewer which can also give you a publication quality visualization  of these four tracks. I have tried popular genome browsers like IGV, IGB, tview and many more. I'm not satisfied with any of these softwares. It would be nice if I can visualize each read only once, but somehow (either by width, heatmap or numbers beside them) highliting is abundance/depth at each position. So, is there any other better viewers or packages in R or Python which I can customise to my need? Thank you in advance.

]]> anushreenarjala@rocketmail.com