Question: gene and exon number from bed file
0
gravatar for bioguy24
4.1 years ago by
bioguy24190
Chicago
bioguy24190 wrote:

I am trying to add the gene_name to a bed file and I think the method I used below is using the gene_id instead. Is it possible to get the gene_name and maybe exon_number? Thank you .
 

1.  wget ftp://ftp.sanger.ac.uk/pub/gencode/release_21/gencode.21.annotation.gtf.gz
 
2.  gunzip --stdout gencode.v21.annotation.gtf.gz \
    | gtf2bed - \
    | grep "exon" \
    > gencode.exons.bed

3.  bedmap --echo --echo-map-id-uniq epilepsy70_medex_edit.bed gencode.exons.bed > output.bed
genecode_exons.bed
chr1 11868 12227 ENSG00000223972.5 . + HAVANA exon . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

output.bed (as of now)

chr1 43408884 43409004
|
chr1	43424253	43424373
|ENSG00000198198.11
chr1	154540492	154540612
|
chr1	154541927	154542093
|ENSG00000163239.10

epilepsy70_medex_edit.bed
chr1	40539722	40539865
chr1	40542489	40542609
chr1	40544221	40544341
chr1	40546054	40546174
chr1	40555071	40555194
bedops • 1.4k views
ADD COMMENTlink written 4.1 years ago by bioguy24190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1709 users visited in the last hour