I'm running into a problem with the output from bowtie mapping for
illumina reads. I've been testing bowtie with a subset of my illumina
reads with the intention of estimating the percent of *uniquely* mapping
reads represented in my library, ie., non-repetitive reads.
I've run bowtie on this small subset (~2000 reads) with and without the -m
option specified with n=1 and I get many fewer mappable reads with -m
specified, but if I ask galaxy to "Write all reads with a number of valid
alignments exceeding the limit set with the -m option to a file (--max)",
the file always comes up empty.
Where did all those suppressed reads go?
thanks for any help you can offer,
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