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I created a fasta file of 50 nt sequences and ran bowtie-build to create an index.
bowtie-build fasta.fa fasta_index
This generated 6 files correctly. Next, I aligned a set of reads to the fasta_index.
bowtie fasta_index -t -v 2 reads.fq output.map
Looking at the output.map file, some of the start positions report 200+. How can the start positions be 200+ if the fasta_index sequences are 50 nt long?
bowtie-build fasta.fa fasta_index
This generated 6 files correctly. Next, I aligned a set of reads to the fasta_index.
bowtie fasta_index -t -v 2 reads.fq output.map
Looking at the output.map file, some of the start positions report 200+. How can the start positions be 200+ if the fasta_index sequences are 50 nt long?
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