Dear all,
is velvet (or others) able to use a read twice in the assembly of two different contigs or does velvet need in this case two duplicates of this read?
It could be that in certain genes highly conserved domains are present. In order to be able to assemble the different genes, certain reads could be used more than once. Is this possible in velvet (or others)?
The reason why I ask this is because I filter my dataset for duplicated reads, thereby only keeping the "unique" ones. But I wonder now if I do not lose information by doing this. If velvet (or others) is able to use reads more than once, the filtering is fine; if not, I should keep all my reads.
Any comments more than welcome.
Many thanks in advance,
Steven
is velvet (or others) able to use a read twice in the assembly of two different contigs or does velvet need in this case two duplicates of this read?
It could be that in certain genes highly conserved domains are present. In order to be able to assemble the different genes, certain reads could be used more than once. Is this possible in velvet (or others)?
The reason why I ask this is because I filter my dataset for duplicated reads, thereby only keeping the "unique" ones. But I wonder now if I do not lose information by doing this. If velvet (or others) is able to use reads more than once, the filtering is fine; if not, I should keep all my reads.
Any comments more than welcome.
Many thanks in advance,
Steven
Comment