Sense and antisense metaplot

[Raphael]

Hi all,

I'm struggling to do a metaplot that consider sense and antisense reads.

The idea is similar to what was published here using ngsplot:

I have seen this post here https://groups.google.com/forum/#!searchin/ngsplot-discuss/strand%7Csort:date/ngsplot-discuss/9P3IeodQUYk/8kioSXOFBQAJ -but it is not clear how to perform nowadays with the -SS option.

I have 2 bam files per sample or treatment: one for "+" strand and "-" strand.

Based on this, how can I do it?

Is the only way using -SS opposite and -SS same and then averaging the -SS same of same samples to have sense and -SS opposite of same samples to have antisense and then plotting it by myself?

How can I do the same for standard error?

Is there a more straight forward way?

Best wishes,

[Sarah Muniz Nardeli]

Hi Rafael,

Did you solve the sense/antisense metaplot issue? After a few testes, I am not even sure if -SS opposite means the antisense transcripts. If you have any direction on that, I would appreciate it.

Thank you,

Sarah