Hi Jeremy,<div><br><div>Thanks for your help. I&#39;m mapping reads from one organism to a related but different organism, so some of the parameters I&#39;d like to adjust are to relax mapping stringency -specifically:</div>

<div><br></div><div>-n 3 (allow 3 mismatches in seed)</div><div>-e 250 (allow cummulative phred score of 250 [or some other value depending on read length] for mismatches in remainder of read)</div><div><br></div><div>I&#39;d also like to only report alignments that are unambiguously mapped to a single location, so:</div>

<div><br></div><div>-m 1</div><div>--best on</div><div>--strata on</div><div><br></div><div>It sounds like I need to read the documentation again, but it didn&#39;t look at first glance like I could specify these things.</div>

<div><br></div><div>Jeremy<br><br><div class="gmail_quote">On Wed, Nov 16, 2011 at 12:18 PM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

<div style="word-wrap:break-word"><div>Jeremy,</div><div><br></div><div><div class="im"><blockquote type="cite">My apologies if this has been covered before but I am using Galaxy Main and wonder if, when running TopHat, you can modify the mapping parameters used by Bowtie? </blockquote>

<div><br></div></div><div>Not all Bowtie parameters can be modified when running Tophat. Which parameters are you looking to modify and why?</div><div class="im"><br><blockquote type="cite">It seems that the full parameter list for TopHat pertains only to the reads that aren&#39;t mapped by Bowtie (the reads spanning splice junctions). </blockquote>

<div><br></div></div><div>This should not be the case. For instance, documentation for the max-multihits discusses multiple hits when mapping reads junctions/segments:</div><div><br></div><div><a href="http://tophat.cbcb.umd.edu/manual.html" target="_blank">http://tophat.cbcb.umd.edu/manual.html</a></div>

<div><br></div><div>If you&#39;re seeing different results, it may be a bug that could be discussed with the Tophat authors: <a href="mailto:tophat.cufflinks@gmail.com" target="_blank">tophat.cufflinks@gmail.com</a></div>

<div class="im"><br><blockquote type="cite">Is there a way to access the full parameter list of Bowtie through TopHat? </blockquote><div><br></div></div><div>Not currently.</div><div class="im"><br><blockquote type="cite">

Or perhaps run Bowtie directly, then feed this into a TopHat run?</blockquote><br></div></div><div>I don&#39;t think this is possible b/c Tophat uses the reads that map initially to build the coverage islands and then uses these islands to generate an index of potential splice junctions.</div>

<div><br></div><div>Best,</div><div>J.</div><div><br></div><div><br></div><div><br></div><br></div></blockquote></div><br></div></div>