Arabidopsis Thaliana genomic features

Question

[dzisis1986]

I am wondering where i can find bed files for genomic features (TSS, TTS, CpG sites) of Arabidopsis Thaliana. I want to use a tool for 4Cseq analysis called w4Cseq. In order to be able to analyze T. Arabidopsis data i need cytobands, TSS, TTS, CPG and GENE files in bed format.

Thank you

Dimitris

[lieven.sterck]

what did you try already? or where have you looked for it?

Can we assume you had a look at the TAIR and/or AraPort websites but did not find what you're looking for?

[dzisis1986]

Yes i checked at the TAIR but i didnt find it. Unless if i don't know how to find it! Do you have a link with that ? Thank you in advance

Answer 1

[lieven.sterck]

I'm not sure if you can get the features you request as in a nice set by themself but here is the link to download data from AraProt (including BED12 format) . Starting form that info you should be able to deduct things like TSS TTS (not sure about the CpG though)

[dzisis1986]

I manage to create a bed file from gff3 file of arabidopsis thaliana but thats all . I dont know how to go from this to TSS or TTS or CPG.

[lieven.sterck]

indeed., unless they are specifically annotated as such (which they probably are not) you will have to proxy them. for TSS take the 5' end coordinate of the mRNA, for the TTS take the most 3' end of the mRNA (mRNA coordinates should be present in the gff3 file). I can't immediately give you a proxy for the CpG ones.