Hi, I have a workflow on the published workflow list (called "Bristol workflow to get....") which takes sam files and separates the unique from the non unique mapped reads. This might help in the sense I have used this kind of approach to count up the number of unique vs non uniquely mapped reads. Let me know if you need more info. Cheers, David On 23 Mar 2011, at 02:30, karlerhard@berkeley.edu wrote:

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

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