counting gene distance

Question

[MEITUO]

Does anyone knows how to count the distance of the gene in the genome, and is there any tool available?

[rpolicastro]

By distance, what do you mean more specifically?

[ATpoint]

Please provide a representative input example and an example of intended output.

[MEITUO]

i mean in a genome, which has many genes, so how to calculate the physical distance of two neighboring gene

[GenoMax]

By subtracting the start coordinate of second gene from end of first.

Answer 1

[Alex Reynolds]

If you have to deal with multiple overlapping elements, it isn't as straightforward as subtracting coordinates.

You can use a tool like closest-features on a BED-formatted file of gene annotations.

Get genes, e.g. for human (hg38):

$ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.basic.annotation.gff3.gz \
    | gunzip -c \
    | convert2bed --input=gff - \
    > gencode.v35.bed

For purposes of demonstration, I'll cut out details like strand and GFF3-specific keys:

$ cut -f1-5 gencode.v35.bed > gencode.v35.c1t5.bed

To calculate the distances of closest features, use the gene annotations file as both reference and map files:

$ closest-features --closest --dist --no-overlaps  gencode.v35.c1t5.bed gencode.v35.c1t5.bed > answer.bed

The result will look something like this, depending on what you use as your gene annotations file:

$ head answer.bed
chr1    11868   12227   exon:ENST00000456328.2:1    .|chr1  12612   12697   exon:ENST00000450305.2:3    .|386
chr1    11868   14409   ENSG00000223972.5   .|chr1  15004   15038   exon:ENST00000488147.1:10   .|596
chr1    11868   14409   ENST00000456328.2   .|chr1  15004   15038   exon:ENST00000488147.1:10   .|596
chr1    12009   12057   exon:ENST00000450305.2:1    .|chr1  12178   12227   exon:ENST00000450305.2:2    .|122
chr1    12009   13670   ENST00000450305.2   .|chr1  14403   14501   exon:ENST00000488147.1:11   .|734
chr1    12178   12227   exon:ENST00000450305.2:2    .|chr1  12009   12057   exon:ENST00000450305.2:1    .|-122
chr1    12612   12697   exon:ENST00000450305.2:3    .|chr1  12974   13052   exon:ENST00000450305.2:4    .|278
chr1    12612   12721   exon:ENST00000456328.2:2    .|chr1  12974   13052   exon:ENST00000450305.2:4    .|254
chr1    12974   13052   exon:ENST00000450305.2:4    .|chr1  13220   13374   exon:ENST00000450305.2:5    .|169
chr1    13220   13374   exon:ENST00000450305.2:5    .|chr1  13452   13670   exon:ENST00000450305.2:6    .|79

This result is delimited by a pipe character (|). The first field is the reference element (gene annotation). The second field is the nearest, non-overlapping gene annotation. The third field is the signed distance between reference and nearest elements. A positive value is downstream of the stop coordinate of the reference element. A negative value is upstream of the start coordinate of the reference element.

For more detail:

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html