I have about 100 million reads from a SOLiD run. I am trying to align them using bwa and I got 0 alignments. What am I doing wrong here? Here are the commands that I am using
~/software/bwa-0.5.9/bwa aln -n 6 -t 6 -o 2 -c ~/genomes/hsap/hg19.fa sampleTF5.fastq.gz ~/software/bwa-0.5.9/bwa samse ~/genomes/hsap/hg19.fa sampleTF5.sai sampleTF5.fastq.gz |samtools view -bS -|samtools sort - sampleTF5
About 40% of the reads align using Bioscope so I know that at least some reads should align. The index was created using -c so it is a colorspace index.
ETA: Couple of reads from the fastq file
@853_2_23 T10201001101112312122022330313023.22201032232203002 + .06%8+23,-/,740&+2,&(*+&26%&%'';!%'(&)':2((,,-'%(. @853_2_76 T00221112202322220011002232000222000212301132232001 + &<*(%'?'&'&5)*'%%%&('-'(()-')&)&%)*'/%%&%'%(%&&'&%