Question: Sanger sequencing chromatogram aligned to reference gene
0
gravatar for vujex
12 days ago by
vujex0
vujex0 wrote:

I did Sanger Sequencing on 10 samples targeting one specific gene to see whether we detect a particular SNP. We did forward, reversed and tested three primer sets so there are quite a lot samples in total.

Now, I am wondering if there is a quick way to generate chromatograms of the data so for all the 10 samples, aligned to the reference genome? This would save a lot of time compared to the conventional way (aligning via Blast ect.).

ADD COMMENTlink modified 12 days ago by trausch1.6k • written 12 days ago by vujex0

We Used to do it using sequencher. It is manual and laborious but we went through hundreds of chromatograms to verify the sequencing.

ADD REPLYlink written 12 days ago by Asaf8.5k

You can do this in Snapgene pretty easily. I'm not aware of a commandline tool for something like this however.

ADD REPLYlink written 12 days ago by Joe18k
0
gravatar for GenoMax
12 days ago by
GenoMax95k
United States
GenoMax95k wrote:

I am wondering if there is a quick way to generate chromatograms of the data so for all the 10 samples, aligned to the reference genome?

I assume you already have the chrromatograms having sequenced the samples using sanger otherwise there is no way to generate the chromatograms.

There are two programs (novoSNP and Tracy) mentioned in the answers for this past question (A: Sanger sequencing data analysis ) that should work with your sequence files. Both are free compared to commercial applications.

ADD COMMENTlink modified 12 days ago • written 12 days ago by GenoMax95k
0
gravatar for trausch
12 days ago by
trausch1.6k
Germany
trausch1.6k wrote:

Indeed, you can use tracy as a command-line application to process them in batch or use the online web applications:

ADD COMMENTlink written 12 days ago by trausch1.6k
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