Hi all, and sorry if I bother again the mailing list with my issues.I need to reassemble an assembly (a mapping, precisely), which I edited using consed, working on the ACE output.
My case matches the point 3 of "Using backbones to perform a mapping assembly against a reference sequence" in the short usage manual: Backbone sequences will not not be assembled together! That is, if a sequence of the backbones has a perfect overlap with another backbone sequence, the will still not be merged. So I did this manually. Now I still have a lot of contigs, mainly made by 454 sequences, which are clearly combinable together, but its impossible do it manually in a reasonable frame of time. Since I worked on the ACE file, which could be the right strategy to reassemble 454-contigs?
And I'm still trying to convert the ace file into the caf format. I was thinking to reassemble with mira using the caf file as input, after filtering out contig with less than 4x of coverage. I used phred2caf and roche454ace2caf, but both produce a caf file which convert_project doesn't like. With the latter script, by Bernd Senf, I got this message when I apply convert_project:
fos10Contig6.c is a sequence used as backbone, but actually it is present in the caf file!Converting from caf to: caf First counting reads:[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]Now loading and processing data: [0%] Searched for read fos10Contig6.c but did not find it? Unable to find Read in PoolInternal logic/programming/debugging error (*sigh* this should not have happened).Please contact the author: bach@xxxxxxxxxxxx "fos10Contig6.c" ->Thrown: Readname not found in hash as expected? ->Caught: int32 CAF::getCafAssembledFrom() Program aborted. Program aborted.
any suggestion is wellcome! cheers stefano -- Dr. Stefano Ghignone Istituto per la Protezione delle Piante, Sez. Torino - CNR c/o Dpt. Plant Biology, University of Turin V.le P.A. Mattioli, 25 I-10125 Turin Italy Phone: +39 011 6502927 ext. 48 Fax: +39 011 6705962 e-mail: stefano.ghignone@xxxxxxxx- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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