#285 Not catching an obvious alignment

bowtie (178)

Hi all,

I am trying to understand so bowtie1 behavior that is perplexing. I've got a certain number of reads that align EXACTLY to a reference sequence. Bowtie does not catch it. Bowtie2 catches it, as does BWA, but Bowtie1 does not. I've attached a 1 read paired end fastq and the reference sequence for duplication. Running bowtie-0.12.9

Nothing crazy parameter-wise:
bowtie-build definite_reference.fa definite_reference.fa
bowtie -S -p 10 /mnt/scratch/jpowers/indexes/h_sapiens/contaminome_v1.fa -1 read1.fq -2 read2.fq
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments

bowtie2-build definite_reference.fa definite_reference.fa
bowtie2 --very-sensitive-local -x definite_reference.fa -1 read1.fq -2 read2.fq
1 reads; of these:
1 (100.00%) were paired; of these:
0 (0.00%) aligned concordantly 0 times
1 (100.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times

Similar output if I don't use the --very-sensitive-local

Probably not important, but I'll remark on it here is that when using --very-sensitve-local option, the cigar string for read 1 is 74M1S, without that option it is 68M3I4M



  • Jason Powers

    Jason Powers - 2013-05-09

    Note: The first bowtie1 command was run on definite_reference.fa. I cut and pasted the wrong reference in there, sorry


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