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identify Gencode genes residing in 1-Mb intervals

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

rna-seq
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updated by Ram Ram • written by hana hana

1 answer

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)

Edit:

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

• 1 views • link
updated by Ram Ram • written by PoGibas PoGibas

Thank you so much

• 1 views • link
updated by Ram Ram • written by hana hana

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

• 0 views • link
updated by Ram Ram • written by PoGibas PoGibas

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