Hello there,
It appears that the content of the ACE file is quite inconsistent with the fasta files content and the 454NewblerMetrics file:
Sometimes, the fna files are empty, 454NewblerMetrics has no contigs nor isotigs but...
The corresponding ACE will have a hundred contigs/isotigs with a mean depth of 10 000 and minimum size of 120.
Looking into the ace file show that these sequences are fulled with "*".
So I wonder: is the ace file a temporary (unfiltered) one ?
Another point: it seems that running a de novo assembly starting from fasta and not sff improve the assembly quality (less "*" in the sequences)
Anyone has seen that ? Is there some Newbler options to use for fixing this ?
Cheers
It appears that the content of the ACE file is quite inconsistent with the fasta files content and the 454NewblerMetrics file:
Sometimes, the fna files are empty, 454NewblerMetrics has no contigs nor isotigs but...
The corresponding ACE will have a hundred contigs/isotigs with a mean depth of 10 000 and minimum size of 120.
Looking into the ace file show that these sequences are fulled with "*".
So I wonder: is the ace file a temporary (unfiltered) one ?
Another point: it seems that running a de novo assembly starting from fasta and not sff improve the assembly quality (less "*" in the sequences)
Anyone has seen that ? Is there some Newbler options to use for fixing this ?
Cheers
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