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Old 07-10-2014, 09:20 AM   #8
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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uloeber,

1) BBNorm was designed to prioritize discarding of reads that appear to contain errors, so typically, there are fewer low-frequency kmers after normalization. When you normalize, you can set "hist=khist_input.txt" and "histout=khist_output.txt". The first file will get the frequency histogram of kmers before normalization, and the second one after normalization, so you can see how the process changed the distribution.

2) I'm glad it was helpful!

3) If the input is interleaved, the program will autodetect that, as long as the reads follow the standard Illumina naming patterns, so it should be fine. I will update it to print a message indicating whether it is processing the data as paired or not. You can force a file to be interpreted as interleaved with the "interleaved=t" flag.
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