I am new in the field of computational biology. This questions might answered somewhere else but I could not find by searching. How can I extract annotation for genes from a GTF file that are more than 200 bp apart from neighboring genes? I was looking into bedtools for this but most functions in bedtools compare two files but I would like to compare genes within my annotation file. It will very helpful if someone can suggest how can I do this. For example:
Input files:
I ensembl gene 335 649 . + . gene_id "YAL069W"; gene_source "ensembl"; gene_biotype "protein_coding";
I ensembl gene 538 792 . + . gene_id "YAL068W-A"; gene_source "ensembl"; gene_biotype "protein_coding";
I ensembl gene 1807 2169 . - . gene_id "YAL068C"; gene_name "PAU8"; gene_source "ensembl"; gene_biotype "protein_coding";
I ensembl gene 2480 2707 . + . gene_id "YAL067W-A"; gene_source "ensembl"; gene_biotype "protein_coding";
Output:
I ensembl gene 1807 2169 . - . gene_id "YAL068C"; gene_name "PAU8"; gene_source "ensembl"; gene_biotype "protein_coding";
Thank you so much.
Thank you so much. Very good solution.