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!!
Oliver
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o.hickman •
Hi, 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.
Best,
Agata
I tried this and I would like to add something extra. Also select Track:- UCSC. I obtained multiple lines w.r.t. original co-ordinates in .bed so I collapsed it using bedtools: bedtools map -a original.bed -b ucsc_based_gene_list.bed -c 5 -o collapse
Post processing and filtering redundancies, You could try bedmap as explained by @ Alex Reynolds in this post C: how to get gene names and gene id given co ordinates from ensembl its fast and elegant.
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Is the gene name in your file itself? Though
KHDRBS1may be onchr1thanchr7if that line is correct.Hi, Sorry, that column is the name of the experiment. The gene name is definitely not in there. Can you help? O.
You can use biomaRt package to get the genes' chromesome information, then you can map your bed file to gene symbols or gene IDs.