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Old 08-03-2021, 01:08 PM   #55
andy_muan
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Join Date: Aug 2021
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Default Multiple Samples for BBNorm

Hi Brian -- How would this work with paired-end reads? Would it be okay to concatenate all forward and all reverse reads then run BBNorm?

Quote:
Originally Posted by Brian Bushnell View Post
At this point, BBNorm does not accept multiple input files (other than dual files for paired reads). You would have to concatenate them first:

cat a.fastq.gz b.fastq.gz > all.fa.gz

...which works fine for gzipped files. Most of my programs can accept piped input from stdin, but not BBNorm since it needs to read the files twice.
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