Dear All,
I did run a file.fasta using bowtie2 with a command bellow
./bowtie2 -x ~/tan_analysis/rice1 -U ~/tan_analysis/GBS20130709_S1_L001_R1_001.fastq -S GBS_test.sam
1604137 reads; of these:
1604137 (100.00%) were unpaired; of these:
1583639 (98.72%) aligned 0 times
16736 (1.04%) aligned exactly 1 time
3762 (0.23%) aligned >1 times
1.28% overall alignment rate
my question is why the overall alignment rate very low/
I did run a file.fasta using bowtie2 with a command bellow
./bowtie2 -x ~/tan_analysis/rice1 -U ~/tan_analysis/GBS20130709_S1_L001_R1_001.fastq -S GBS_test.sam
1604137 reads; of these:
1604137 (100.00%) were unpaired; of these:
1583639 (98.72%) aligned 0 times
16736 (1.04%) aligned exactly 1 time
3762 (0.23%) aligned >1 times
1.28% overall alignment rate
my question is why the overall alignment rate very low/
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