Question: Visualize paired end reads
0
gravatar for Chirag Nepal
5 months ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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 !!

rna-seq alignment paired-end • 181 views
ADD COMMENTlink modified 5 months ago by jbalberge140 • written 5 months ago by Chirag Nepal2.2k

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by Pierre Lindenbaum129k

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 !

ADD REPLYlink written 5 months ago by Chirag Nepal2.2k
1
gravatar for genomax
5 months ago by
genomax87k
United States
genomax87k wrote:

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.

ADD COMMENTlink modified 5 months ago • written 5 months ago by genomax87k
0
gravatar for jbalberge
5 months ago by
jbalberge140
France/Nantes
jbalberge140 wrote:

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

ADD COMMENTlink written 5 months ago by jbalberge140
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