Extracting a full length gene from illumina reads?
Hi all,
I've recently started a phd and I'm fairly new to all this so apologies if this is the wrong place to post this question.
I'm trying to see if it's possible to extract full length gene sequences from an illumina sequenced metagenome using partial gene sequences as a guide.
I have several partial novel gene sequences PCR amplified from a soil environment with degenerate primers.
I also have paired end Illumina sequence data from the same environment (about 12 million reads).
Blasting the partial sequences against the illumina data I can see that the sequences are there along with many highly related sequences.
What I'd like to be able to do is extract at least one of the full length genes in order to design primers for the full gene or have it synthesized.
is something like this even possible without doing whole genome assembly? any help at all would be greatly appreciated.
And again apologies if this is the wrong place.
Thanks
Jonathan
I've recently started a phd and I'm fairly new to all this so apologies if this is the wrong place to post this question.
I'm trying to see if it's possible to extract full length gene sequences from an illumina sequenced metagenome using partial gene sequences as a guide.
I have several partial novel gene sequences PCR amplified from a soil environment with degenerate primers.
I also have paired end Illumina sequence data from the same environment (about 12 million reads).
Blasting the partial sequences against the illumina data I can see that the sequences are there along with many highly related sequences.
What I'd like to be able to do is extract at least one of the full length genes in order to design primers for the full gene or have it synthesized.
is something like this even possible without doing whole genome assembly? any help at all would be greatly appreciated.
And again apologies if this is the wrong place.
Thanks
Jonathan