Visualize paired end reads

Question

[Chirag Nepal]

Hi There

Any suggestion on how to visualize the connection between two reads/fragments of paired end RNA-seq data. The screenshot of the description is posted here

One paired ends are map to the genome by using BLAT (shown on top as black bar). Aligned reads from STAR are shown in blue and red. There is blue and red fragment that corresponds to the above black fragment. I want to show a connecting line between these two black bars or between it's corresponding blue/red. thanks !!

[Pierre Lindenbaum]

Hello Chirag Nepal!

It appears that your post has been cross-posted to another site:

enter link description here

This is typically not recommended as it runs the risk of annoying people in both communities.

[Chirag Nepal]

Hi Pierre, I added the twitter url to show the image of what i was describing. In that case, i will now remove the twitter url from here. Not gonna do that again. thanks !

Answer 1

[GenoMax]

If you use IGV, you can right-click in IGV window and then choose "View as pairs". Unless I completely missed what you are asking.

Answer 2

[jbalberge]

Pairoscope draws arcs between reads of paired-end sequencing data http://pairoscope.sourceforge.net/