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Old 04-08-2015, 07:51 AM   #64
Location: UK

Join Date: Jan 2014
Posts: 75

Originally Posted by joshquick View Post
When you decreased the SPRI ratio you increased the insert size and we found bowtie2 behaves weirdly above 500bp inserts with the default settings. You might want to change your bowtie2 settings or try bwa-mem:
Actually this is a very good point that I knew about (from reading your post earlier) but recently forgot about. It turns out that part of the poor mapping of the recent run (aside from issues with quality that Illumina are investigating) are due to the difference between running Bowtie2 in Ugene (with default settings) and my coworker running Bowtie2 on a cluster with -X 1000.

Default settings gives about 75% alignment, whereas with X-1000 we achieved 94% (still not as good as some other libraries - 97% - , so we think that probably the low overall sequence quality in the last run is affecting mapping).

Last edited by M4TTN; 04-08-2015 at 08:03 AM.
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