Question: chipseq identification of enrichment of preselected genes
gravatar for rob.costa1234
3.1 years ago by
United States
rob.costa1234250 wrote:

I have a list of 10 genes that i want to find level of enrichment in a public data set. So I downloaded FAStq files and run the alignment with Bowtie, Macs for peaks. Now my question is how should i Specifically check the status of these selected 10 genes in analyzed data. I can take an indirect approach that annotate MACS peaks first and see overlap of the selected genes. I was wondering is there any direct approach of sub-setting Peaks data corresponding to my 10 selected genes. I only have gene ids- hugo gene names.

Thanks for the input.

selected genes chipseq • 693 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by rob.costa1234250

Assuming that you mean enrichment OF some transcription factor/histone modification ON the preselected genes here is one thing you can do.

Just upload the peak.bed file from MACS output and the alignment file (SAM/BAM) directly onto some genome browser. Again, assuming that the genome browser that you use, also has the genome and gene list annotated (else you may have to do it by yourself), you can just search for your preselected genes and take a look at the peak profile on each genomic locus one-by-one.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Satyajeet Khare1.6k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2298 users visited in the last hour