Checking regions with high density of SNPs
Hi,
I calculated number of SNPs in non-overlapping windows in each chromosome. I found regions with extreme numbers of SNPs in compare to other windows. How can I check this region/window? What software can I use to check if this region contain many genes or sth else? I would like do it based on GFF file or sth similar because the same I want to do for windows with no SNPs.
Thank u.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Amplicon sequencing and unwanted amplicons
written by misterie
-
Is there some good software to align/compare fasta sequences in my PC
written by silas008
-
SNP absolute number or density between chromosomes
written by misterie
-
Merging 2 GFF files
written by misterie
-
mean Tajima's D value
written by biosol
-
snpEff assigned all variants as modifier intergenic
written by misterie
-
Psuedoautosomal regions in reference genome
written by misterie
-
Problems with exome coverage at HRNR gene
written by ognjen011
-
Intersect versus Count Overlapping Intervals
written by cellochick09 •
-
Overlapping Reads In Window Approach
written by Vikas Bansal
this answer might be useful: A: Mapping SNP position to gff file
Try using IGV software (https://software.broadinstitute.org/software/igv/download) or if your lab/company will pay for it, Geneious (https://www.geneious.com/). You should be able to visualize the SNPs in IGV once you generate your .genome file (or find it online) and have a VCF file.