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Old 03-19-2017, 01:02 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 819
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2) If Yes, is it better to align reads by yourself, using BWA, or just download BAM file? Would be there some differences in result?
That depends on your experience, available time, and domain knowledge.

I generally prefer doing my own read cleaning and alignment, because then I know precisely the process that was used for read filtering and mapping. From my own memory of how submissions work, I think the BAM files in SRA are aligned using whatever method the experimenter decided to use.
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