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 ___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
