Hi,
Maybe I'm missing some of the bowtie options, but when I map my reads against a pile of contigs (together in a reference file) and when I make the same mapping but only with one contig alone, I do obtain a different number of mapped reads ("reads with at least one reported alignment") for that contig. These are the options I normally use:
bowtie -f --sam --best
Any idea?
Thanks
Maybe I'm missing some of the bowtie options, but when I map my reads against a pile of contigs (together in a reference file) and when I make the same mapping but only with one contig alone, I do obtain a different number of mapped reads ("reads with at least one reported alignment") for that contig. These are the options I normally use:
bowtie -f --sam --best
Any idea?
Thanks
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