Question: How to get list of different bases and their positions from an alignment?
0
gravatar for SaltedPork
8 months ago by
SaltedPork80
SaltedPork80 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 • 230 views
ADD COMMENTlink modified 8 months ago by WouterDeCoster36k • written 8 months ago by SaltedPork80
1

Hi SaltedPork,

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

Cheers,
Wouter

ADD REPLYlink written 8 months ago by WouterDeCoster36k

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 8 months ago by finswimmer8.9k

Hi, just the sequences i'm comparing.

ADD REPLYlink written 8 months ago by SaltedPork80
1

Hi,

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

fin swimmer

ADD REPLYlink written 8 months ago by finswimmer8.9k

they are about 92% similar, ~700 base difference

ADD REPLYlink written 8 months ago by SaltedPork80

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

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax60k
2
gravatar for WouterDeCoster
8 months ago by
Belgium
WouterDeCoster36k 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 8 months ago by WouterDeCoster36k
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