Profiles stratified by strand

[Xavi Sole]

Hi all,

is there a way to plot TSS profiles stratified by strand? I would like to use ngsplot with my GRO-Seq data and I would like to see whether we observe divergent transcription (which occurs on the opposite strand and in the opposite direction next to the TSS of the genes).

Thanks!!

Xavi.

[Li Shen]

Hi Xavi,

ngs.plot automatically reverse the coverage if it sees a TSS on reverse strand. That means, the left side is always 5' and the right side is always 3'. So if your gro-seq is reverse to the gene transcription, you'll see a reversed pattern (not sure what is looks like). There is no need to stratify genes based on strands. 

I'm not entirely if I understood you correctly. Just post if you have more questions.

- L

[Xavi Sole]

Hi Li,

Sorry I didn't make myself clear. Let's see if I can do it better now:

1) Let's imagine a gene located, say, in the forward strand. For the GRO-Seq (as well as for the RNA-Seq) we will see reads mapping downstream the TSS (5'->3' direction). That's the "regular" transcription.

2) However, thanks to assays such as the GRO-Seq, for many genes a pattern of "divergent transcription" has been observed. That means that there's transcriptional activity upstream the TSS (3'->5' direction) and in the opposite strand that the gene is being transcribed. This is what is depicted in the figure that I attach, section A.

I understand that ngsplot merges the reads from both strands, is that right? That's why I was asking if it was possible to segregate both strands in order to plot one in the upper part of the graph and the other in the lower part, such that it's easier to depict things such as this divergent transcription phenomenon.

Thanks a lot for your help!

Xavi.

El dimecres 29 de maig de 2013 13:12:31 UTC-4, Li Shen va escriure:

[Xavi Sole]

Sorry here's the plot I was talking about!

Thanks!

Xavi.

El dimecres 29 de maig de 2013 15:11:10 UTC-4, Xavi Sole va escriure:

[Li Shen]

I see. That's much clearer. 

But sorry ngs.plot does not support that function. I'll certainly consider adding this kind of functionality in the future.

To not disappoint you, you can use ngs.plot to achieve part of your goal. For example, you can certainly separate your bam file into two: forward.bam and reverse.bam. Then do a plot for both bam files. Both coverage plots will be shown above the axis. But it's conceptually the same.

If you want further customization, you can also extract those data from the output .zip file and do plot by yourself in Excel, etc. You basically use ngs.plot as a convenient tool to calculate coverage but not its visualization.

I hope this helps.

[Raphael]

Hi all,

This is a quite old trend. But did the situation change?

Is it possible now to plot it on a strand specific manner? If yes, can someone paste an example here?

Many thanks