Defining Precisely The Genomic Context Based On A Position

Question

[Nicolas Rosewick]

Hi,

How can I define the genomic context (so what are the genes in the neighbourhood) based on position ( like a bed file ).

The informations I want to know is :

• Is the position in an intron of a gene ? If yes, which intron (and the distance from the exons)
• If the position is intergenic : which gene are upstream and downstream (and distances)
• If there are several genes that are overlapping the position, report them and where it is (which intro or exon)

Edit > I add a little picture to explain the expected results :

So the expected results for position 1 ( I omit the position and gene real coordinates but they have to be in the results also )

Position1 Gene_A exon1 50 intronPosition
Position1 Gene_B exon2 -100 intronPosition

For position2

Position2 Gene_A exon3 200 intergenicPosition
Position2 Gene_C exon1 -100 intergenicPosition

I konw that bedops closes-feature is a good start but I'm stuck with the overlapping genes and to check if the position is intergenic or not ?

Anyone can give me ideas and/or advices to solve this problem

Thanks a lot,

N.

[Pierre Lindenbaum]

have a look at Is a genome position in an exon or intron?

Answer 1

[Pierre Lindenbaum]

I quickly wrote something: see https://github.com/lindenb/jvarkit#biostar81455 .it finds a record in UCSC knownGenes, get all the overlaping transcripts and output the nearest exons.

$ ant biostar81455 && echo -e "chr22\t41258261\nchr22\t52000000\nchr22\t0" | java  -jar dist/biostar81455.jar
chr22    41258261    uc003azg.2    41253084    41258785    POSITIVE    Exon 2    41257621    41258785    0
chr22    41258261    uc011aox.2    41253084    41305239    POSITIVE    Exon 1    41253084    41253249    -5012
chr22    41258261    uc003azi.3    41253084    41328823    POSITIVE    Exon 1    41253084    41253249    -5012
chr22    41258261    uc003azj.3    41255553    41258130    NEGATIVE    Exon 1    41255553    41258130    -131
chr22    41258261    uc010gyh.1    41258260    41282519    POSITIVE    Exon 1    41258260    41258683    0
chr22    41258261    uc011aoy.1    41258260    41363888    POSITIVE    Exon 1    41258260    41258683    0
chr22    52000000    uc011asd.2    51195513    51227614    POSITIVE    Exon 4    51227177    51227614    -772386
chr22    52000000    uc003bni.3    51195513    51238065    POSITIVE    Exon 4    51237082    51238065    -761935
chr22    52000000    uc011ase.1    51205919    51220775    NEGATIVE    Exon 1    51220615    51220775    -779225
chr22    52000000    uc003bnl.1    51205919    51222087    NEGATIVE    Exon 1    51221928    51222087    -777913
chr22    52000000    uc003bns.3    51222156    51238065    POSITIVE    Exon 3    51237082    51238065    -761935
chr22    52000000    uc003bnq.1    51222224    51227600    POSITIVE    Exon 4    51227322    51227600    -772400
chr22    52000000    uc003bnr.1    51222224    51227781    POSITIVE    Exon 4    51227319    51227781    -772219
chr22    52000000    uc010hbj.3    51222224    51238065    POSITIVE    Exon 3    51237082    51238065    -761935
chr22    0    uc002zks.4    16150259    16193004    NEGATIVE    Exon 8    16150259    16151821    16150259
chr22    0    uc002zkt.3    16162065    16172265    POSITIVE    Exon 1    16162065    16162388    16162065
chr22    0    uc002zku.3    16179617    16181004    NEGATIVE    Exon 1    16179617    16181004    16179617
chr22    0    uc002zkv.3    16187164    16193004    NEGATIVE    Exon 5    16187164    16187302    16187164

[Nicolas Rosewick]

Thanks. But I don't work in human. I've a gtf and bed file with all my exon position.

Answer 2

[Ashutosh Pandey]

You can use Annotation software like snpEff and Annovar and annotate your genomic positions.