read-qualities lost in Mosaik-processing

[tczy]

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

[sklages]

Hi Till,

ACE files never contain read qualities. These are stored in the phd files. That's one big drawback of ace formatted alignments.

You should write your own phd.ball file containing all all reads of the alignments from the original sff file(s).

scf files (as fake chromatograms) are created on the fly from consed solely for editing purposes.

cheers,
Sven

[snownebula]

Hi Till,

The read qualities are really only accessible via the formats available in MosaikText.

Most file formats in MOSAIK support the notion of alignment qualities. Saving your alignments to the following file formats will preserve the alignment qualities:

axt, bed, SAM, & BAM

The Eland file format in MosaikText as well as the ace and gig formats in MosaikAssembler do not support alignment qualities.

Cheers,

// Michael

[tczy]

Hi Sven and Michael,

thank you for your helpful replies.

At the moment, we (i.e. me and a colleague) are using the resulting gig files for SNP detection with the GigaBayes. My colleague who is in charge of the GigaBayes analysis, told me he gets out the read-qualities he needs out of the gig-files, so we are fine for the moment.

Anyhow, in case I'll do some efforts like those suggested by Sven at a later stage of the project, I'll post this here.

Thanks again!

Cheers,

Till

Till

[Clody23]

Hi,
I'm working with the latest version of Mosaik (1.0.1384) to carry out a reference guided assembly of a data set of 454 sequences (Titanium). With this version is possible to obtain .qual files from the .ace or .gig files (the output of MosaikAssembler) adding the -cf parameter, but I have a problem! In this .qual file I notice that scores associated to each base are not phred-like, but they range from 0 to 9. I would like to know if they are the result of a revaluation of the quality score made by Mosaik (on the basis, I think, of the alignment quality) or if the sequences are worst! I discard this hypothesis cause I've checked the quality scores before applying Mosaik to my dataset and i verified that most of them are up to 30!
Thanks in advance for your help!
Cheers,
Claudia