A quick google I found:
http://www.biostars.org/p/6682/
the qseqtofastq C++ program http://www.dna.bio.keio.ac.jp/~krisp/qseq2fastq/ has to be compiled by scons, and I encountered some compiling problem. I gave it up and used this java program http://sourceforge.net/projects/snpeff/files/qseq2fastq.jar/download
Usage:
zcat myfile.qseq.tgz | java -jar qseqtofastq.jar -phred64 > myfile.fastq
it took me around 1 hour to finish the conversion of a 600MB tgz file on the computing cluster (single cpu 4GB ram).
I did have a problem at the end:
Exception in thread "main" java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 8
at ca.mcgill.mcb.pcingola.Qseq2Fastq.main(Qseq2Fastq.java:51)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 8
at ca.mcgill.mcb.pcingola.Qseq2Fastq.main(Qseq2Fastq.java:43)
I counted the lines of the fastq file (divided by 4) and the original qseq file , and they are equal. So, I went ahead and mapped the fastq file with bowtie.
