Gene list from bed file
I have a .bed file with Chromosomal coordinates instead of gene names in columns 1, 2 and 3. How do I get the coesponding gene list from this information?
chr7 120792856 120792910 K562_rep01 1000 + 5.486570215 14.23664891 -1 -1
Thanks in advance!!
you also can use bedtools intersect. From the online manual:
bedtools intersect allows one to screen for overlaps between two sets of genomic features.
One set is your bed file, the second file could be a GFF/GTF file with the gene model of your organism.
I think you can do it by UCSC Table Browser:
Select group: Genes and Genes predictions, RefSeq, hg19/hg38
Define regions in region field (chr:start-end), then select output format: all fields from selected table, get output.
At the end of text file you will have field name2 - gene name.
I think it is possible to filter all unnecessary informations from this file and leave only gene name, transcript etc. and save in BED file.
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