Question: Re: Output File For Bowtie Suppressed Reads (-M/--Max)
0
karlerhard@berkeley.edu • 90 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
ADD COMMENT
• link
•
modified 7.7 years ago
by
David Matthews • 630
•
written
7.7 years ago by
karlerhard@berkeley.edu • 90
