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

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

sample output of annotation.txt 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!!!

rna-seq lncrna hommer bed gtf
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updated by jordi.planells jordi.planells • written by mathavanbioinfo mathavanbioinfo

1 answer

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

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written by jordi.planells jordi.planells

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