How To Create A Read Density Profile Within A Interval?

Question

[Ophélie]

HI!

I need some help: I have to create density profile with a window specific of 1kb (how many time a sequence is detected after NGS method). I have to use SAM and BEDtools, I think I can use genomeCov in BEDtools but I don't have genome reference.

So, if anybody is abble to help me...

Thanks

[Steve Lianoglou]

What programming langauge(s) are you familiar with?

[Ophélie]

I have to use 'BEDtools' to do that it's really specific.

Answer 1

[Istvan Albert]

There are many similar questions on BioStar, although I admit these are not that straightforward to find as the terminology is somewhat fuzzy. Perhaps this search helps:

http://www.biostars.org/search/?q=density+plots&t=top&submit=

In general the answer is to use a tool like HTSeq like so:

http://www-huber.embl.de/users/anders/HTSeq/doc/tss.html

[Zev.Kronenberg]

It appears the top link is generating a 404, bummer.