Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
What does the '#bin' mean in UCSC table browser output file? gary Bioinformatics 2 06-28-2012 06:28 PM
how to get annoation file from UCSC table browser? zhaowei Bioinformatics 3 05-17-2011 08:11 AM
Galaxy vs. UCSC Genome Browser Table Queries? jnfass Bioinformatics 2 09-02-2010 10:56 AM
UCSC Table Browser: Please tell me there is an easier way... jjw14 Bioinformatics 5 07-19-2010 07:39 AM
aggregating data for features using UCSC Table Browser M.N. Bioinformatics 0 05-17-2010 12:02 PM

Thread Tools
Old 06-30-2021, 05:57 PM   #1
Junior Member
Location: South Korea

Join Date: Oct 2020
Posts: 2
Default How do I convert a list of ncRNA genes into annotation using UCSC table browser

Hello Guys,

I have analyzed a set of ChiP-seq data for a Transcription factor. I have my BigWig files and a list of genes names (ncRNA) I got from my overlap analyses. So I want to visualize the enrichment of my TF on these set of ncRNA genes. The tool I am using for generating the heatmap is deeptools2 (computeMatrix and plotHeatmap). So my question is how do I convert these list of ncRNA genes into an annotation file (BED format) using the UCSC Table Browser or any other tool?

Also, I how can I get the complete annotation file for non-coding RNA KnownGenes (BED format) so I can visualize their enrichment around promoter site of my TF ChiP-seq data.

Can anyone kindly assist with useful information on how to go about this?

Thank you.
tiptophamza is offline   Reply With Quote

annotation file, chip-seq analysis, heatmap, ncrna, ucsc genome browser

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:14 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO