coordinates to hg19 refseq gene name

[cmccabe]

Is there a tool or script that can convert chromsome, start, and end to chromosome, start, end, gene?

Input: (txt file)
chr1 955542 955763
chr1 957570 957852
chr1 976034 976270

Output:
chr1 955542 955763 ...
chr1 957570 957852 ...
chr1 976034 976270 ...

... is the gene name. Thank you.

[dpryan]

There are a number of options for this. One option would be to use GenomicRanges and GenomicFeatures in R. You can also use bedtools or bedops (just use one of the commands that yields the closest feature in a second file and then reparse the output to contain only what you need).

[cmccabe]

coordinates to hg19 refseq gene name

Here is what I am trying to do:

In BedTools get a list of gene names from a list of coordinates:
chr1 955542 955763
chr1 957570 957852
chr1 976034 976270

(is there a command in BedTools you recomend)?


create example.bed in UCSC

In BedTools:

mergeBed - i example.bed > merged_example.bed

intersectBed -a example1.bed -b example2.bed > intersected_example.bed


Basically, I am trying to find a subset of probes (example.bed) in a panel of ~4600 genes (example1.bed). Thank you.

[chrchang]

The PLINK 1.9 resources page describes how to construct this type of gene list file from UCSC Table Browser output:

https://www.cog-genomics.org/plink2/resources#genelist

(It sounds like you can skip the final "resort by gene name" steps.)