How to extract upstream and downstream of lncRNA in particular range?

Question

[mathavanbioinfo]

Hello All I am trying to extract the upstream and downstream genes of differentially expressed lncRNAs. Initially, I converted the merged gtf file to bed file using bedops tool, then I used hommer Perl script to convert it annotation file using the following command

perl annotatePeaks.pl sample_peak.bed Genome.fasta -gft genome.gft >homer_annotation.txt upstream genes 300 kb downstream genes -300 kb

https://ibb.co/42s7Thj Then sorted the 300 kb in TSS column, further how do I get the nearby gene names, please check this file and guide me!!!

Answer 1

[jordi.planells]

bedtools flank and bedtools closest might be helpful for your analysis. Might be worth to take a look at them!