Question: How to get list of different bases and their positions from an alignment?
0
gravatar for SaltedPork
3 months ago by
SaltedPork70
SaltedPork70 wrote:

I am aligning two viral genomes which I am expecting to be >90% similar. I would like a list of the changes (from one base to another) and their locations in the genome. Which program(s) can I use to achieve this? I have already tried lastz's --census option, but it only tells you if a base is aligned, not whether it is identical. Thanks.

alignment • 150 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster31k • written 3 months ago by SaltedPork70
1

Hi SaltedPork,

I have reopened this question, there is not really a need to delete it.

Cheers,
Wouter

ADD REPLYlink written 3 months ago by WouterDeCoster31k

Hello,

is your data from a sequencing project or do you just have the reference sequences you like to compare?

fin swimmer

ADD REPLYlink written 3 months ago by finswimmer4.5k

Hi, just the sequences i'm comparing.

ADD REPLYlink written 3 months ago by SaltedPork70
1

Hi,

how have you done the alignment? How does the output look like?

fin swimmer

ADD REPLYlink written 3 months ago by finswimmer4.5k

they are about 92% similar, ~700 base difference

ADD REPLYlink written 3 months ago by SaltedPork70

That does not answer @finswimmer's question about format of the output.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax54k
2
gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster31k wrote:

If I understand correctly you want to align to reference genomes and find the differences. If so, you could try minimap2 to align both using the -cx asm5 option. Scripts are available in that repo (paftools) to get the differences.

ADD COMMENTlink written 3 months ago by WouterDeCoster31k
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: 1628 users visited in the last hour