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Old 06-23-2011, 01:25 PM   #2
Senior Member
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

What was your experiment design? Standard Illumina mate-pair? Read length? Also how did you reverse complement and what was the bwa command line arguements?

I've done standard Illumina MP preps, reverse complemented with fastx-toolkit and aligned with standard parameters using bwa before with good success. See below

133724796 in total
0 QC failure
45170770 duplicates
121800898 mapped (91.08%)
133724796 paired in sequencing
66862398 read1
66862398 read2
102897270 properly paired (76.95%)
115119322 with itself and mate mapped
6681576 singletons (5.00%)
3387642 with mate mapped to a different chr
2495203 with mate mapped to a different chr (mapQ>=5)
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