retrieve chromosome index

Question

[niutster]

Hi, I have a file contains some chromosomal indexes such that it has chromosome name, sequence start on chromosome , sequence end on chromosome. I want to find which biological roles are related to these sequences, for example gene, TF, promoter,... but i dont know how can i do it. I try UCSC genome browser but it only finds genes.

Thanks

[GenoMax]

Sounds like you can use bedtools intersect with your file (which sounds like it is already in BED format) with a GFF format annotation file for the genome you are interested in. See the help link here.

[niutster]

Thanks, but i did not understand in which path can find these information, please explain more.

Answer 1

[Alex Reynolds]

One way to do this is to use BEDOPS gff2bed and bedmap.

For example, if you are working with GRCh38, you could get GENCODE annotations and convert them from GFF3 to BED:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.chr_patch_hapl_scaff.annotation.gff3.gz \
    | gunzip --stdout - \
    | gff2bed - \
    > annotations.bed

Then if your sequences are in a sorted BED file called sequences.bed, for example:

$ bedmap --echo --echo-map sequences.bed annotations.bed > answer.bed

This would give you your sequence and any annotations that overlap that sequence. Other --echo-* operations are available; see bedmap --help or the documentation online for more details.