Simulated overlapping paired end reads for 16S
Hi, I have a fasta files with 16S sequences from 20 different species. I would like to generate paired end reads (overlapping).
I was trying to use the following command form the bbmap package:
randomreads.sh ref=20_species_16S.fasta out=read.R1.fq.gz out2=read.R2.fq.gz paired reads=100000 length=250 mininsert=400 maxinsert=500
Would that randomly assign the same number of reads to each species in the ref file ?? If i have 20 species i would expect at least 5000 reads per species ?? Is that correct ??
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I think so, but if you want to be absolutely sure you could generate the reads independently for the 20 species and then use
reformat.shwithsamplereadstarget=5000with each and then merge the resulting files. You would want to setmaxinsert=450if you want to ensure overlap.