Question: How to extract upstream and downstream of lncRNA in particular range?
0
gravatar for mathavanbioinfo
8 weeks ago by
India
mathavanbioinfo60 wrote:

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!!!

lncrna hommer rna-seq bed gtf • 178 views
ADD COMMENTlink modified 8 weeks ago by jordi.planells330 • written 8 weeks ago by mathavanbioinfo60
1
gravatar for jordi.planells
8 weeks ago by
jordi.planells330 wrote:

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

ADD COMMENTlink written 8 weeks ago by jordi.planells330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1639 users visited in the last hour
_