Hi,
I am currently using the Mosaik software to process some 454 transcriptome data. I am importing BOTH fasta and quality files using MosaikBuild, sth like:
> MosaikBuild -fr reads.fasta -fq reads.qual -out reads.dat -st 454
the same thing for the reference:
> MosaikBuild -fr reference.fna -fq reference.qual -oa reference.dat
Then, I do the assembly following the instructions (i.e. MosaikAligner, MosaikSort, MosaikAssembler). In the resulting ace files there are are no read-qualities assigned for the individual bases of the reads. There are links to scf-files and phd-files, but these scf files are not to be found anwyhere.
Did anyone of you encounter similar problems or even better has an idea how to overcome these?
At the moment I am considering writing a script to add the qualities from my individual read-files by hand, but I feel this would be a bit clumsy.
Thanks in advance for your help,
Till
I am currently using the Mosaik software to process some 454 transcriptome data. I am importing BOTH fasta and quality files using MosaikBuild, sth like:
> MosaikBuild -fr reads.fasta -fq reads.qual -out reads.dat -st 454
the same thing for the reference:
> MosaikBuild -fr reference.fna -fq reference.qual -oa reference.dat
Then, I do the assembly following the instructions (i.e. MosaikAligner, MosaikSort, MosaikAssembler). In the resulting ace files there are are no read-qualities assigned for the individual bases of the reads. There are links to scf-files and phd-files, but these scf files are not to be found anwyhere.
Did anyone of you encounter similar problems or even better has an idea how to overcome these?
At the moment I am considering writing a script to add the qualities from my individual read-files by hand, but I feel this would be a bit clumsy.
Thanks in advance for your help,
Till
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