New to Newbler

[Resa7362]

You know what... I didn't actually have my files in the right format. Thanks for asking that simple question! Hopefully now this will work.

Sorry for wasting people's time!

[twaddlac]

Could you post the format of you reference sequence?

Fasta should be:
>name
ACTCAGCTAGCTACT

[Resa7362]

I am trying to use Newbler to align my 454 sequencing results to a reference sanger sequence. I have already gotten my 454 sequences partitioned into separate files based on quality, length, and my MIDs.

I have tried using the Mapper and the Amplicon analyzer. I want to just look at the different variants within my individuals and compare them to each other and the reference sequence. Does anyone have a simple explanation as to how to do this?

The manual that I have looked at is dense, and ultimately, not very helpful for my situation. I tried to upload my reference sequence to the reference tab in the Mapper, but it says that I have the wrong format. I put it in as a FASTA file (which by reading the manual I thought was OK, but it apparently is not.)

Any sort of help would be greatly appreciated!