How to extract gene_id from a specific locus?

[angel-sakura]

Hello everyone,
I'm looking for updtream or downstream transciption factors and lncRNA of some specific genes. Just wandering is there any command or method that can extract gene_id from cuffdiff or cuffmerge results based on a defined locus.
For example, gene_A locus is on "scaffold1:3267260-3298933" (the data can be found from cuffdiff or cuffmerge output). I want to get all gene id from "scaffold1:1267260-5298933" (2 million base pairs of upstream and downstream).
Could someone shed light on this please?
Thank you very much in advance.

[GenoMax]

I assume this is not a genome that has annotation available? If you do have annotation then it would be possible to get the information you need with BEDTools and the associated GTF file.

If this data is from a genome available at UCSC or Ensembl then you could use the table browser (UCSC) or Biomart (Ensembl) to get the information.

[angel-sakura]

Thank you for your reply!
However, I am working on non-model organism, therefore, I do not have the annotation.
We have the genomic sequence (.fa file) but it is not available on UCSU or other website.

[GenoMax]

In that case you will have to do annotation in order to identify the genes before you can get the information you want. There are annotation pipelines available that can help. CEGMA or MAKER2 are options for Eukaryotic genomes. Prokka is recommended on the forum for prokarytic genomes.

[angel-sakura]

That is what I need, a name of command.

Thank you very much !!