Re: sliding window of coverage

[Assaf Gordon]

(Just in case - I'm forwarding to the bedtools mailing list).

I'm not sure if there's tool that does all of that one one step,
but you can generate a BED file with sliding windows ("bedtools makewindows") and then calculate the coverage for each window ("bedtools coverage") - I think that will give you want you need.

-gordon


Sergei Manakov wrote, On 05/25/2012 05:44 PM:
> Dear Gordon,
>
> I tried to post a question to BedTools google group, nothing appears
> on the webpage or in e-mail. I actually tried to post something
> twice, as I couldn't understand what is going on at first. Sorry
> about that. Should I just be more patient, or maybe something is
> wrong with my registration?
>
> My question was on the way to make either wig files or bedgraph files
> that would describe coverage per floating window of arbitrary
> size/step. Could you let me know if you know of a program that could
> do that? your suggestion would be very helpful.
>
> thanks, Sergei

[Sergei Manakov]

Thanks for your suggestion and posting the message.

I also was considering pre-computing sliding windows. Thanks for suggesting a program for that, and it's good to know that such approach is sound.

Also hopefully it will be more clear on what is going on with my bedtools posts. Do you usually e-mail the mailing list, or actually create "New post" in the google group page? I did the latter, maybe it's not an optimal way of doing things...


thanks,
Sergei

[Aaron Quinlan]

Hi Sergei,

Sorry for your troubles with the mailing list.  I believe the Google lists require you to become a member of the list in order to post directly.  Have you done that?

Best,

Aaron

[Sergei Manakov]

hi Aaron,

Yes, I did join the group "bedtools-discuss", and in fact after a few hours my posts where eventually e-mailed to the mailing list. So probably I just have to be more patient in the future. Sorry about that and thanks very much for checking on me.

Regarding my actual question, Gordon suggested to pre-compute sliding windows for a genome and then estimate coverage in these intervals with "bedtools coverage". This sounds like it's definitely going to work. Looking at the help, I can't yet figure out if there is a way to compute intervals on the fly and output bedGraph?

thanks,
Sergei

--
Sergei (Siarhei Manakou) Manakov

California Institute of Technology

+1 626 395 3593