Phrap / Consed

Stefan Weckx sweckx at uia.ua.ac.be
Mon Jul 10 10:41:26 EST 2000


Hi all,

I've two questions about Phrap / Consed:
- it's possible to compile the Phrap "longreads/manyreads" version, and
it's also possible to compile gcphrap for the Staden package (with the
patch from the Staden website). Has anyone ever tried to combine these 2
ways of compiling, so that the longread/manyread version of Phrap can be
integrated into the Staden package? If so please let me know how!
- The *'s which appear in the consensus sequences in Consed are not
written in the fasta file with contigsequences generated by Phrap. Does
anybody know a possibility to get these *'s out of the consensus in
Consed (since these *'s get a basenumber in Consed which I want to
avoid) or to get them in into the fasta file with contigsequences?
Result must be a perfect match between the basenumbers in Consed and the
number of each base in the fasta file (if you would count them).

thanx
Stefan
 
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Stefan Weckx
Bioinformatics unit
Department of Molecular Genetics
University of Antwerp (UIA)		 
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