Hello,
I am trying to align paired end reads from Solexa using Bowtie, the command is below. But, this does not work and we get 4% reads aligned. If we use the sequences/reads not paired we get 96% reads aligned. We have tried using different combinations of --ff, --fr, etc.... This makes no difference. What are we doing wrong?
./bowtie -p 12 --sam mus -1 ../working/s_1_1_sequence.fastq,../working/s_2_1_sequence.fastq,../working/s_3_1_sequence.fastq -2 ../working/s_1_2_sequence.fastq,../working/s_2_2_sequence.fastq,../working/s_3_2_sequence.fastq ../working/s_123.sam
I am trying to align paired end reads from Solexa using Bowtie, the command is below. But, this does not work and we get 4% reads aligned. If we use the sequences/reads not paired we get 96% reads aligned. We have tried using different combinations of --ff, --fr, etc.... This makes no difference. What are we doing wrong?
./bowtie -p 12 --sam mus -1 ../working/s_1_1_sequence.fastq,../working/s_2_1_sequence.fastq,../working/s_3_1_sequence.fastq -2 ../working/s_1_2_sequence.fastq,../working/s_2_2_sequence.fastq,../working/s_3_2_sequence.fastq ../working/s_123.sam
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