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,


The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to