I am trying to map Illumina paired-end reads of the Bacillus subtilus natto genome to the reference genome. Everything is running smoothly, but I am only able to get 50 mapped reads at best. Here are my commands:
./fastq-dump --split-files ~/DRR000001.sra #Gives Forward and Reverse files ./fastq_quality_filter -Q33 -q 30 -p 70 -i ~/DRR000001_1.fastq -o ~/natto1_trim.fastq ./fastq_quality_filter -Q33 -q 30 -p 70 -i ~/DRR000001_2.fastq -o ~/natto2_trim.fastq bowtie-build -f bsubtilisnatto.fasta natto bowtie natto -1 natto1_trim.fastq -2 natto2_trim.fastq pair.sam --al pair.align --un pair.unmapped -l 20 -X 300 --fr -q -t --sam -n 3 --solexa-quals -p 8
The filter leaves about 700,000 and 400,000 reads. The reference fasta file is about 4 Mbp. This may be low, but surely it's not 50 mapped reads low. I've tinkered with the bowtie command, using --rf, --ff, lowering thresholds, ommitting --solexa-quals, all to no avail.
Your help would be much appreciated!