Question: how to distinguish between artifacts and real indels?
0
gravatar for yelekley7
8 months ago by
yelekley70
yelekley70 wrote:

Hello,

I’m working with multiple sequences (fasta format) of the same human gene (exons 2,3,4). Each sequence is about 5300 nucleotides long. When I import the sequences into MEGA I can see that there are multiple “-“ deletions and “|” insertions in random places. These sequences came from a software that assigned the genotype allele to each sequence. When I view multiple sequences that presumable belong to the same genotype allele, I see that they don’t exactly align due to these “artifacts” .

Should I assume these are artifacts indels and remove them before doing the alignment? My goal is to find new variants outside the exon 2. How would I know these are variants and not artifacts?

Any advice will be greatly appreciated.

Thanks

alignment • 210 views
ADD COMMENTlink written 8 months ago by yelekley70
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: 776 users visited in the last hour