Question: Get the genes between certain chromosomal position
0
gravatar for akij
18 months ago by
akij90
akij90 wrote:

I know this is very common questions. But my input list is huge. So it would be nice if I can just input my whole list and output.

So I have a huge list of chromosomal positions in a excel file that looks like below. I want to find the genes between each start and end positions of chromosome.

chr       start          end        prob_no
1   196792690   196829513       36823
1   248572774   248633821       61047
2   41011303    41024125        12822
2   52516787    52554404        376176
3   189645889   189653199        7310
3   193160173   193165114        4941

How can I get the gene lists? It would be also nice if I could get the output like this

chr       start          end        prob_no  genes
1   196792690   196829513       36823      gene1, gene2.....
gene • 629 views
ADD COMMENTlink modified 18 months ago by Alex Reynolds26k • written 18 months ago by akij90

Hi akij,

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Cheers,
Wouter

ADD REPLYlink written 18 months ago by WouterDeCoster34k
1
gravatar for Alex Reynolds
18 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

BEDOPS bedmap does exactly what you need, outputting results in the format you want:

$ bedmap --echo --echo-map-id-uniq positions.bed genes.bed > answer.bed

If you have gene annotations in GFF or GTF format, you can convert them via BEDOPS gff2bed or gtf2bed, e.g.:

$ bedmap --echo --echo-map-id-uniq positions.bed <(gff2bed < annotations.gff) > answer.bed

Or:

$ bedmap --echo --echo-map-id-uniq positions.bed <(gtf2bed < annotations.gtf) > answer.bed

The default criteria for mapping is one or more bases of overlap between reference and annotation intervals. Add --fraction-map 1 if you want only the gene annotations reported that map entirely within the reference interval.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Alex Reynolds26k
0
gravatar for genomax
18 months ago by
genomax58k
United States
genomax58k wrote:

Take a look at bedtools intersect (documentation) that you can use with a GTF file for your genome (with the genes in it).

ADD COMMENTlink written 18 months ago by genomax58k
0
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

I have a huge list of chromosomal positions in a excel file

"huge" and "excel" are antinomic

have a look at the UCSC table browser to get the intersection with a gene track: https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SimpleIntersection

ADD COMMENTlink written 18 months ago by Pierre Lindenbaum114k
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