Hi!
I've read a lot of posts similar to this but I've not seen (or may have missed) a good solution of how to find all genes in a region when you have multiple (200+ regions).
For example, I have a list of regions like this
chr3:56953782-58953782
chr3:229305477-231305477
chr13:48536705-50536705
chr10:62754024-64754024
chr6:31633697-33633697
chr6:31608932-33608932
chr6:31587588-33587588
UCSC's interface is great, but it gives me a list of all results in one file without indication of which rows belong
#hg19.knownCanonical.chrom hg19.knownCanonical.chromStart hg19.knownCanonical.chromEnd hg19.kgXref.spDisplayID hg19.kgXref.geneSymbol
chr3 56761445 57113336 Q9NR81-2 ARHGEF3
chr3 56974067 56994880 ARHGEF3-AS1
chr3 57094468 57109460 SPT12_HUMAN SPATA12
chr3 57124009 57199403 I17RD_HUMAN IL17RD
chr3 57231943 57234280 HESX1_HUMAN HESX1
chr3 57261764 57307498 DP13A_HUMAN APPL1
chr3 57310555 57326132 C9JX97_HUMAN ASB14
chr3 57327726 57530071 DYH12_HUMAN DNAH12
chr3 57541980 57547768 PDE12_HUMAN PDE12
Ensambl's biomart is great too, but similar problem.
Is there a way I can get something along the lines of:
region Genes
chr3:56953782-58953782 GENE1
chr3:56953782-58953782 GENE2
chr3:56953782-58953782 GENE3
chr3:229305477-231305477 GENE4
chr3:229305477-231305477 GENE5
Thank you!
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brighteyes1017 •
2 answers
You can get the genomic locus of the gene with BioMart, which you can then reference back to your input list, but that's non-ideal.
An alternative is to use the Ensembl REST API overlap endpoint. You can then program in any language you like to run through your list and print with your loci and genes.
Looking at your list, these are all single bases. Are they variants? In which case, have you considered using the VEP instead?
If you transform your list of regions to bed format (sed + awk for instance) and you download the gene definitions you want from UCSC's TableBrowser for instance in bed format too, then a simple bedtools command would do:
sed 's/[:-]/\t/g' regions.txt \
| awk 'OFS="\t"{$2--; print}' \
| bedtools intersect -wao -a - -b genes.bed
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