bowtie and solexa paired ends wont align

[michy]

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

[Dethecor]

Align them unpaired

You could also try to shorten the reads to avoid overlapping of the pairs (which is probably the cause of the bad alignment).

So, I have not examined that in detail but I think it happens if the fragments are shorter than 2 times the read size so that overlapping occurs.

Also, if you get ~96% aligned if you do it unpaired then that is a reasonable result and can be used just like this.