Hi all,

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,

karl