Question: plot the number of variations within a certain window
1
gravatar for Sara
10 months ago by
Sara150
Sara150 wrote:

we have used crispr-cas9 technology which was followed by whole genome sequencing. I have got the SNPs and INDELs frequency and now trying to plot how many variations are within 10 bp of a NGG or NAG sequence in the geome. do you have any suggestion about how the plot should look like? or how to make such plot?

snp next-gen • 168 views
ADD COMMENTlink written 10 months ago by Sara150

I suppose they should look like at Fig1 from here https://www.nature.com/articles/nature14221 (if they are not super-rare, otherwise I question the usefullness of such visualization). I would not analyse indels because for me it is totally unclear how to count their frequencies within your provided sequences. As I answered in another thread, you can count your occurences, create SEG file and visualize in IGV - https://software.broadinstitute.org/software/igv/SEG - otherwise I'd recommend to use R - but! - it is impossible to see anything in a human genome with 10bp resolution, you will just get a total mess (of course if your plot will not be of width of 1 million of pixels)

ADD REPLYlink modified 10 months ago • written 10 months ago by German.M.Demidov1.9k
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: 1424 users visited in the last hour