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gene name from bed file using R language of cell lines

what packages of r can be used to analyse the bed files. i want to align the bed file to genome data to get the gen name of the bed file. the syntax mention below has suggested by many but its not working over

annotatePeaks.pl  <peak/BED file> <genome>   > <output file>
r rna-seq
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updated by Ram Ram • written by abhilashreddy495 • abhilashreddy495

C'mon man, with that kind of sloppy and undetailed question, you'll not get any elaborate response. Provide some details what data you have, what you've tried and what the final goal is.

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written by ATpoint ATpoint

Try again, but this time, be polite.

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written by Emily Emily

That comment was directed at ATpoint, not you. ATpoint is right, you have not included enough details in your question, but their way of saying it was incredibly rude.

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written by Emily Emily

You are not wrong, but you could have phrased it much better. It may not be obvious for new users which information is important. Also language barrier problems may make questions unclear. The last thing we want is that this forum becomes a 'hostile' environment which scares away those users which need help the most.

Besides reactions like this (which I would call "too direct") we absolutely value your contribution to biostars. Thank you for being an active member!

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written by WouterDeCoster WouterDeCoster

1 answer

the syntax mention below has suggested by many but its not working over

annotatePeaks.pl <peak bed="" file=""> <genome> > <output file="">

That is not R, that is part of a separate program called HOMER.

There are several example methods of annotating .bed files (e.g. getting the gene names for coordinates in the file) listed here:

https://github.com/stevekm/annotate-peaks

Including methods using R packages.

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written by steve steve

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