How to locate a locus on the genome and get the Exon/Intron No.

Question

[shiyang93]

HI, I have a set of locus: chr2:123456-234567......，now I want to know if this locus is on a gene, if it is, then on which exon/intron? Because there are too many locus, viewing on the genomebrowser one by one is not practical. I also have tried softwares such as ANNOVAR, ONCOTATOR, but they only tell me whether it is exonic or intronic...， without the exon/intron No. (It is possible they tell me but I do not find.) I also try to find this in a gtf download from gencode, but also have no answer. Could anyone recommend some software? Or other methods? Thanks!

[cpad0112]

Try any genome browser like ensembl, NCBI, UCSC (online) or IGV (standalone)

[shiyang93]

But there are too many locus, need a lot lot lot of time to view them one by one.

[Jean-Karim Heriche]

Use EnsEMBL's perl API.

Answer 1

[EagleEye]

I will recommend you to

1) Use bedtools to get overlapping transcripts using GFF as reference gene annotation (use the same as your required genome version)

2) For those transcripts check number of exons and introns, Example: A: How to get the number of exon within genes from GRCH37 reference (For introns per transcript, number of exons minus 1).