Mosaik alignment

[chienchi]

I would like to get the unmapped reads to do other analysis.

MosiakAligner (version:1.0.1367) has an option (-rur) to store unaligned reads in a FASTQ file. But I can not get correct decimal quailty score in that fastq using MAQ fq_all2std.pl. I observed the problem is the negative score.

Here is the command I used to mapping and get unaligned reads.

MosaikBuild -fr test.solexa.fasta -fq test.solexa.qual -out
test.solexa.fasta.mosaik.dat -st illumina
MosaikAligner -in test.solexa.fasta.mosaik.dat -out test.mosaik.aligned.dat
-ia fasta.ref.dat -hs 15 -mm 6 -mhp 100 -act 13 -rur test.unalinged.fastq

Expected output
>GAIIX_6_1000055:8:1:0:1821
-3 1 -2 -2 2 -3 -5 11 -3 -5 -3 -3 1 -1 -5 20 4 5 -2 -5 5 4 -1 8 0 5 -2 -3
-2 -3 -2 1 4 6 -1 4 2 1 -2 -4 9 2 -1 -3 4 0 14 -4 -3
Observed:
@GAIIX_6_1000055:8:1:0:1821 (mate 1, length=49)
CTGCCTNACNAGAANCGAANCTCCGCCGCCCCACTAACTCCTTTACCGC
+
^^"^_^_#^^^\,^^^\^^^^" ^\5%&^_^\&% )!&^_^^^_^^^_"%' %#"^_^]*# ^^%!/^]^^

The ascii code is longer than the length of sequence (49).

I try to understand the ascii code for negative quality score. The compact
form of fastq should be one acsii code to quality score mapping. But now it
is two ascii codes.
-5 => ^\
-4 => ^]
-3 => ^^
-2 => ^_
-1 => space

Do you have any suggestions to convert it back to correct decimal quality score?

Thanks,
Chien-Chi