How To Get Tss From Wormmart?

Question

[UnivStudent]

Just wondering if anyone knows how to get the Transcription Start Site (TSS) data from the wormmart? The data has been deposited by the modENCODE project but I'm not sure how to accurately extract it on a per gene basis. I know it looks like individual annotations in a genome browser track on wormbase but I'm wondering how to get it related to genes and transcripts? Any help would be appreciated!

Also open to solution that don't include wormmart.

[KCC]

You can do this via bioconductor. The ChipPeakAnno package.

Answer 1

[Obi Griffith]

Does this Biomart query give you what you want? I.e., The transcript start for every transcript/gene in ensembl for c. elegans.

http://www.ensembl.org/biomart/martview/e62d75fa07f1db92d7655d9634baad0e?VIRTUALSCHEMANAME=default&ATTRIBUTES=celegansgeneensembl.default.featurepage.ensemblgeneid|celegansgeneensembl.default.featurepage.ensembltranscriptid|celegansgeneensembl.default.featurepage.transcriptstart&FILTERS=&VISIBLEPANEL=resultspanel

Follow link and hit results button to see results.

[KCC]

One thing to be aware of. The last time I checked, wormmart and ensembl have two different sets of worm genes. Not completely different, but it seemed that a few dozen more were in one, but not the other. I think this is because wormmart is more closely linked with wormbase. If I have more time, I will get precise numbers. (You are pulling data here from ensembl.)

[Obi Griffith]

This is good to know. But, do you know how to construct a similar query at wormmart? I can see how to get genomic start coordinates for genes but not transcripts.

[KCC]

I never use the website, the way you are using it, but the wormmart version of biomart, looks quite similar in terms of interface, http://caprica.caltech.edu:9002/biomart/martview/e5194dfcdf86b169d0823f9c48acc4f5

[Obi Griffith]

Yes. The interface looks very similar. But, the options you can choose in terms of attributes are completely different and I can't find transcript start site listed anywhere. Thus I can find no way to get TSSs from wormmart the way you can from biomart. But, I'm probably just missing something.

[UnivStudent]

Thanks everyone for your answers! I think I have enough now to get what I was looking for.