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 07-30-2012, 01:59 PM #1 owenman Junior Member   Location: California, USA Join Date: Aug 2011 Posts: 4 bowtie2 minimum score threshold I am using bowtie2 version 2.0.0-beta7 A careful reading of the bowtie2 manual section for local alignments makes it sounds like the best score you can possibly get is 2 times the read length: "A base that matches receives a bonus of +2 by default." "The best possible score in local mode equals the match bonus times the length of the read." But the very next paragraph says: "In local alignment mdoe, the default minimum score threshold is 20 + 8.0 * ln(L), where L is the read length." This seems contradictory: If a perfect match receives a score of 2 times the read length, how can you ever get a score that is 20 plus 8 times the length? Am I missing something?
 07-30-2012, 02:10 PM #2 nickloman Senior Member   Location: Birmingham, UK Join Date: Jul 2009 Posts: 356 My reading is that it's 20 + 8 * the natural log of the read length.
 07-30-2012, 03:44 PM #3 owenman Junior Member   Location: California, USA Join Date: Aug 2011 Posts: 4 Ah, right. I guess my "careful reading" wasn't careful enough. I wasn't expecting a natural log - I was reading ln(L) as "the length of read L". It's clear now that you point it out. And I also missed the section on writing formulas farther down in the manual: "The available function types are constant (C), linear (L), square-root (S), and natural log (G)." How embarrassing! Thank you, nickloman, for your reply.
 08-01-2012, 04:58 PM #4 cam.jack Member   Location: Canberra Join Date: Jun 2011 Posts: 11 The first paragraph you read is for end-to-end alignment and the 2nd is for local alignment. They are different methods with different scoring systems.
 08-31-2012, 03:59 PM #5 joseph Member   Location: ca Join Date: Feb 2008 Posts: 39 --score-min bowitie2 Hi I am using bowtie2.0.0-beta7 in --local mode to align SE 50 bases reads; I would like to change the parameter --score-min (default in --local mode is G,20,8) to increase the alignment score. Any suggestions? Thank you, Joseph Dhahbi

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