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Old 02-23-2014, 03:17 PM   #2
Senior Member
Location: US

Join Date: Dec 2010
Posts: 415

Dear Brian,

thanks a lot for posting your aligner package.
Thanks to the PacBio option it is not strictly a short read aligner - but for which max read read length would you recommend it (e.g are merged 500 bp Miseq reads OK for the short read version; are PacBio reads longer than the 6 kb mentioned for version 25 allowed for the latest version)?
Would you recommend any specific settings for the alignment of RNA seq reads?

Last edited by luc; 02-23-2014 at 06:10 PM.
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