How do I convert a list of ncRNA genes into annotation using UCSC table browser

tiptophamza · 06-30-2021, 05:57 PM

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.

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06-30-2021, 05:57 PM	#1
tiptophamza Junior Member Location: South Korea Join Date: Oct 2020 Posts: 2	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.