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Old 09-16-2014, 09:32 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by vingomez View Post
Thanks Brian for your effort in providing bioinformatic applications,

As you mentioned in your post, BBsplit can use two paired-end files as input. In addition to the two files; Can I add a third file (e.g. merged read file) as input?
No, you'll have to do that in two runs, one for the paired reads and one for the merged reads. But ultimately that won't affect the output or runtime (other than the fact that the index will need to be loaded twice, and you'll end up with 2 sam files that need to be merged).

P.S. In previous post "java -Xmx29g -cp /path/to/current align2.BBSplit", must said align2.BBSplitter"
Fixed, thanks!
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