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Only outputting one file? #64
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It’s likely that this is an input issue and would be more appropriate on the bioconductor user forum. What does your readspertx look like? |
If it is an input issue, I don't know why I would get a output fasta file for the first sample_01.fasta which is 14G. I have already removed the zeroes from the readspertx. So I don't think it is that. readspertx = round(20 * fastaFile_nozero / 100)` |
What does the following show: head(readspertx) |
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If I’m understanding your query and the output you’ve shared with me, the output file size is within the realm of expectation. The input specified generates one file per sample, since paired=F. If I recall correctly, 47 million 100bp reads stored in fasta format should be >10Gb. If you could let me know a bit more about what your goal of the simulation is (such as simulating 20x coverage of every transcript in the transcriptome) I could try and help you tweak your commands. |
Hi,
I am running polyester using the following code:
simulate_experiment(EnsemblfastaFile, numreps=c(1,1),fold_changes=fold_changes, reads_per_transcript=readspertx, paired=FALSE, outdir="/mnt/lustre/users/k1632479/polyester/simulatedread", distr="empirical", error_model="illumina5", bias="rnaf")
It runs for hours and outputs a large 8 GB fasta file.
I don't understand what I'm running wrong.
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