Is there any software that can highlight or show the paired end reads within .sam file?

Question

[allenyang2003]

I can use Tablet to search the paired end reads one by one. But that would cost a lot of time.

So I wonder if there is any software that will be able to highlight/show the paired end reads within the mapping result ( .sam file). When you point at one read, the paired read will highlight/show the position. Something like that.

Thanks.

Answer 1

[Matt Shirley]

If you look at the 7th and 8th column (RNEXT and PNEXT in the SAM specification) of the SAM file you'll find the mate's chromosome and mapped position. These will be set to * for unpaired reads or reads where the mate does not align.

[allenyang2003]

Thank you so much for your help. I will try it.

Answer 2

[Dan D]

If you're looking for an interactive visualization app, Integrative Genomics Viewer from the Broad can highlight many pairs at once. The same holds true for a similar program, IGB.

[allenyang2003]

Thank you so much. That was really helpful.