On Sat, 06 Nov 2010 10:56:12 +0100, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
On Samstag 06 November 2010 000.calabi.yau.000@xxxxxxxxxxxxxx wrote:I have a question about the possibility to extract only the consensus stretches from (*.ace) assembly files that have at least a coverage of let's say 3. I don't mean the whole contigs but the part of the contig that is covered at least this high. I understand that internal drops in coverage might give 2 or more fragments from a single contig. So lets say the integer stands for coverage: E.g. 111111112344555665453343333222111111111 => 344555665453343333 [...]> Are there programs or scripts (biopython/-perl) that can do sth like this?I fear I lack the necessary programming skills to get this working in a reasonable amount of time...Why look so far away when MIRA has everything aboard to perform that task? :-)The "-v" option of "convert_project" will probably do what you want, fillingup bases with less coverage than specified with "N". convert_project -f maf -t fasta -r c -v 3 input.maf outputfile (or "-f caf" if you want to start from a CAF) B.
Excellent... MIRA is really a great piece of software.Every time I think about a feature that would be cool in an assembler... MIRA has something like it already :-). Very nice. Now I can even mark the potential chimeric stretches inside the contigs for analysis.
Thank you! Have a nice weekend. Markus -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html
