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Old 07-05-2014, 11:35 AM   #4
sdmoore
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Location: Florida

Join Date: Jun 2014
Posts: 10
Default BBnorm target depth setting

Hi Thread/Brian,

I ran BBnorm on a pre-BBduk'd pair of reads. I plan to use the normalized reads for assemblers (Velvet or A5, well, A4 in this case).

./bbnorm.sh in1=R1_bbduk20.fq in2=R2_bbduk20.fq out1=R1_bbduk20_norm35.fq out2=R2_bbduck20_norm35.fq target=35

the opening dialog states that the target depth is 140 on pass 1, then 35 on pass 2.

Why the two passes?

What are the "error reads/pairs/types"?

Do these normalizations typically help a BBmap (or other) run as well?

Thanks.
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