I have a single pacbio read (in the attachment). When I try to align this reads against a PhiX genome (http://www.ncbi.nlm.nih.gov/nuccore/9626372), I retrieve no errors but the quality of this read is broken, and all next reads are not aligned.
When aligning only this read, the output looks like this:
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
The command I use is:
bowtie2 -p 20 -x PhiX --un failedRemoval.fastq -U failedRead.fastq -S /dev/null
The version of bowtie I use is:
bowtie2-align version 2.1.0
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