identify Gencode genes residing in 1-Mb intervals

Question

[hana]

Hi

I would like to make the graph of distribution of expressed genes by chromosome form transcripts.gtf file. I need to extract the Gencode genes residing in 1-Mb intervals along the chromosome.How I can calculate genes residing in 1-Mb intervals?

Any suggestion would be appreciated

Thank you

Answer 1

[PoGibas]

I would solve such problem using bedtools.

1. Divide your genome/chromosome into x bp size windows (have a look at bedtools makewindows);
2. Intersect windows.bed with transcripts.bed (see bedtools intersect)

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Edit:

Before this you have to download chromosome sizes (see Pierre's answer here).

[hana]

Thank you so much

[PoGibas]

If my suggestion worked for you, please accept my answer (and post your thanks as comment and not as an additional answer :-) ).