Hi Anushree,
I am sorry, but your question confuses me. You have already tried the best genome browsers like IGV (as per my working experience). I guess, you can achieve all as IGV displays only one coverage track per alignment with preference and also highlight potential genetic alterations in reads.
Anyway, there are some few more options available in R that, I guess, could be useful:
R genome browser (Rgb): This package is dedicated to memory efficient genome browsing strategies. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser. More at http://bioinformatics.ovsa.fr/Rgb
Apart from that, R package "ggbio" could be useful as well for extending the grammar of graphics for genomic data. More at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html
The rtracklayer package is an interface (or layer ) between R and genome browsers. More at http://svitsrv25.epfl.ch/R-doc/library/rtracklayer/doc/rtracklayer.pdf and http://svitsrv25.epfl.ch/R-doc/library/rtracklayer/html/00Index.html
Thanks and best of luck for your research.
Hi Anushree,
I am not very expert in it, but these wiki list https://en.wikipedia.org/wiki/Genome_browser could be useful. In addition, Python based genome viewer pybamview http://melissagymrek.com/python/2014/01/30/pybamview.html also seems promising.
Cheers
Hi Anu,
I found this interactive web application for visualizing genomic data http://chromozoom.org/ much useful.
Thanks
Thank you everyone for your valuable answers. Finally, I had to agree with Rahul that currently there is no better genome browser than IGV. Still it has some limitations in visualizing small RNA data.
— anushreenarjala@rocketmail.com 3325 days ago