Hi,
I've never done an actual assembly before so I'm hoping someone can give me some advice to a presumably simple task.
I've got some 100base read paired end genome sequence data of an organism where the genome sequence is not known. At the moment, I have a gene of interest in a closely related organism, and all I want to do is use this gene of interest sequence as a template to:
1.Pull out closely matching reads from my data using Bowtie
2.Use those reads to create a scaffold using velvet (?)
3. Use this initial scaffold to then just extend a couple of kb on either side, again with velvet (?)
Basically, I just want to deduce the orthologue with 5',3' UTR from the dataset.
Is my workflow correct?
Should I be using other software?
Can velvet be set to limit assembly to within a defined range from an initial contig/scaffold?
Thanks for any advice.
I've never done an actual assembly before so I'm hoping someone can give me some advice to a presumably simple task.
I've got some 100base read paired end genome sequence data of an organism where the genome sequence is not known. At the moment, I have a gene of interest in a closely related organism, and all I want to do is use this gene of interest sequence as a template to:
1.Pull out closely matching reads from my data using Bowtie
2.Use those reads to create a scaffold using velvet (?)
3. Use this initial scaffold to then just extend a couple of kb on either side, again with velvet (?)
Basically, I just want to deduce the orthologue with 5',3' UTR from the dataset.
Is my workflow correct?
Should I be using other software?
Can velvet be set to limit assembly to within a defined range from an initial contig/scaffold?
Thanks for any advice.
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