Plotting TATA-box frequency over a genomic region

Question

[topalsalih]

Hi everyone,

I have used FIMO by MEME suite to identify locations of TATA-box in the whole yeast genome, and I obtained a .tsv file with locations and scores for TATA boxes. I would like to plot these frequencies over specific sets of genomic locations (I have a bed file for that). Can I do this in the galaxy platform? Or, should I use another platform/software etc?

Thanks so much, S

Answer 1

[Alex Reynolds]

You can extract the sequence information for these BED regions using a tool like bed2faidx.pl and samtools-indexed FASTA files for your yeast assembly.

Once you have converted BED locations to FASTA sequence, you can bring FASTA sequence into a tool like WebLogo to make a sequence logo.

To display frequencies instead of information content, change the y-axis "Units" pull-down menu from "bits" to "probability" before plotting.

Make sure your sequences line up on the TATA box! Or your sequence logo will look like garbage.