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

Join Date: May 2011
Posts: 838

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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