Code:
bowtie2 --threads 4 -q --sensitive --end-to-end --phred33 -x /db/bowtie2/Hsapiens68 -1 fastq_file1 -2 fastq_file1 -S out.sam
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Sure, its:
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@chris -- would you care to share your command line for bowtie2? I'm running into a slightly worse issue, performance wise, and am curious how you're doing it!Leave a comment:
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On/off target rate for whole exome data
Hi all,
I've some human exome data, which I've aligned with bowtie2 as bwa doesn't work (see this post).
Using samtools flagstat I can see ~98% of reads map to the genome. However, only about 60% of those are on-target with 40% off-target. That doesn't seem great.
What kind of on/off-target rates do others see?
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