Bioinformatics newbie question on geneious

[arkilis]

I make use of the innder-built toll from Geneious Pro 5.4. to do SNP detect. The dataset I get are seperated into two parts FWD and REV. I drag and drop all the ab1 files into Geneious. and put the ref I get from ensembl into Geneious too.

I do Tools-> Algin/Assemble -> Map to Reference. The outcome is like in the following pic:



The coverage seems bad, am I doing something wrong?

Thanks

[JackieBadger]

This looks targeted i.e. not random shearing to sequence large regions of the genome.

How was the sequence data generated?
Do you only get hits on that one scaffold?

[arkilis]

This looks targeted i.e. not random shearing to sequence large regions of the genome.

How was the sequence data generated?
Do you only get hits on that one scaffold?

I got the data from client. Why would it have FWD and RVS. Curious..

[JackieBadger]

Before you attempt any analysis you should know what to expect in the data.

1) What sequence data do you expect
2) How was it generated

Only then can you begin to assess if its "good" or "bad" data

[arkilis]

Before you attempt any analysis you should know what to expect in the data.

1) What sequence data do you expect
2) How was it generated

Only then can you begin to assess if its "good" or "bad" data

I see.. Thanks,