Hi again Wences,
i am finishing a metassembly based on several assemblies and have take a look to the scaffold output and have a small question about the fasta labels assigned to some scaffolds. if i make grep ">" files.fasta > labels.txt obtain a
summary of the fasta sequence names and see that there are a first number of sequences labeled as
These are scaffolds present in the primary assembly (or secondary assembly
respectively) that were initially excluded from the metassembly sequence
either because they did not appear in any alignment in the Whole Genome
Alignment preformed with Nucmer or because they were filtered out in the
delta-filter step (also from the MUMMER package); but that were recovered
according to the meta2fasta parameters --keepUnaligned and --keepDF
respectively.
Hi again Wences,
i am finishing a metassembly based on several assemblies and have take a
look to the scaffold output and have a small question about the fasta
labels assigned to some scaffolds. if i make grep ">" files.fasta >
labels.txt obtain a
summary of the fasta sequence names and see that there are a first number
of sequences labeled as
Hi again Wences,
i am finishing a metassembly based on several assemblies and have take a look to the scaffold output and have a small question about the fasta labels assigned to some scaffolds. if i make grep ">" files.fasta > labels.txt obtain a
summary of the fasta sequence names and see that there are a first number of sequences labeled as
these are scaffolds from 0 to 26072 (that is clear)
But then i also see that several scaffolds are labelled as
I am not sure what this means, it refer to repeats or any other kind of correspondence?
i though there are scaffolds provided only by assembly A not present in assembly B but relabeled according to the metassembly sort
is that correct?
thank you in advance
carlx
Hi,
These are scaffolds present in the primary assembly (or secondary assembly
respectively) that were initially excluded from the metassembly sequence
either because they did not appear in any alignment in the Whole Genome
Alignment preformed with Nucmer or because they were filtered out in the
delta-filter step (also from the MUMMER package); but that were recovered
according to the meta2fasta parameters --keepUnaligned and --keepDF
respectively.
Wences
On Mon, Jun 27, 2016 at 6:06 PM, Carlos Llorens cllorens@users.sf.net
wrote: