Hi,
I have 9 genomes, I would like to produce a metagenome like distribution using randomreads.sh. I concatenated genome fasta files in one reference file. Then, ran as below.
../bbmap/randomreads.sh ref=simplified_catgenome.fasta out1=20M.read1.fastq out2=20M.read2.fastq length=125 paired=t metagenome=t genome=9 reads=20000000
However, I would like to know if there is any way I can define the abundances for each genome based on qPCR results and then produce the reads accordingly. Would there be a way to produce reads from each genome separately with the absolute abundances?
Thank you!
1 answer
After you generate a certain number of reads for each genome using randomreads.sh. You can then use reformat.sh
Sampling parameters:
samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
samplereadstarget=0 (srt) Exact number of OUTPUT reads (or pairs) desired.
samplebasestarget=0 (sbt) Exact number of OUTPUT bases desired.
to select desired number of reads from each genome (e.g. 1 M from genome_1, 1.2 M from genome_2 etc). cat the sampled genome files together and then shuffle.sh that file.
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Can you not generate the reads independently and mix them as needed? You can then use
shuffle.shto mix the reads randomly giving you a representative metagenome.I can generate the reads independently. But does shuffle.sh have a function of indicating the abundances? I didnt see any!
I was thinking that you would add known amounts of reads together based on your needs and then simply shuffle them so they represent a mixed metagenome.
Thats my question! How do I add known amount of reads? I will produce randomreads.sh from each genome, then shuffle them , right? But in which step exactly I am adding the known amount of reads for each genome.