Dear all,
I am trying to reconstruct a known full length sequence from contig sequences obtained with Illumina. To do this I tried tblastn using a related sequence as a template.
Using that approach some contig sequences change their translation frame at certain positions. The fact is that using 454 one was able to find homopolymer in that regions, but I am not able to find any specific pattern to explain why the sequencing process was wrong.
I've read something about GGC x G .. but I am not sure to find that pattern into sequences.
Could anyone what nucleotide sequence should be considered to understand this kind of Illumina seqeuncing errors?
Thanks.
I am trying to reconstruct a known full length sequence from contig sequences obtained with Illumina. To do this I tried tblastn using a related sequence as a template.
Using that approach some contig sequences change their translation frame at certain positions. The fact is that using 454 one was able to find homopolymer in that regions, but I am not able to find any specific pattern to explain why the sequencing process was wrong.
I've read something about GGC x G .. but I am not sure to find that pattern into sequences.
Could anyone what nucleotide sequence should be considered to understand this kind of Illumina seqeuncing errors?
Thanks.