How To Make Reads Alignment Visualization

Question

[quge856]

Hi there,

I know there are many NGS alignment viewers (bamview, gap5, igv, mapview, tablet, tview and so on) can make visualization in genome scale. However, what I urgent need is a tool/script/method to show alignment in text, like figures in miRBase (here is a sample). Any one can help me out? Thanks a lot!

[Pierre Lindenbaum]

what's wrong with tview ?

[quge856]

Thanks for input. tview in samtools is good, however, it's not very friendly to snapshot or export result in .png. Meanwhile, it also failed to display reads information (like count number)

Answer 1

[Tky]

Try IGV, load your data and zoon in, you could get a similar figure as the sample file,

[quge856]

Thank you for reply. I tried IGV before. It's awesome, as well as tablet, bamview and so on. Somehow, they make a big fuss over my minor issue. So I decide to handle it by perl script. Anyway, thx a lot