polyester

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Hello, I am trying to simulate reads am an overall curious how long I should expect it to be. I've tried running all chromosomes together on my local device and...

cmill221

Hi polyester, this is a great project! I am currently trying to simulate one sample and I am using the reads_per_transcript as a vector, however, I noticed that the number...

Glenn032787

Hi there, I have a question - potentially bug report - for the simulate_experiment function. I am using polyester to simulated RNA-seq data for a set of features (GTF file),...

vavouri-lab

Is there anyway to specific the total number of reads generated? I know how to specify by transcript but I'm more interested in overall.

nmshahir

Hello, I was attempting to simulate error-free reads with polyester, by using ```simulate_experiment``` function with arguments ```error_model = "uniform"``` and ```error_rate = 0```. But still, when I checked my outputs,...

hl-xue

Support for GFF3

1

Thanks for developing such a useful piece of software! I bumped into an issue when using GFF3 files in Polyester. In GFF3, attributes are separated by and equals signs ("=")...

TBooker

Output of FASTQ or QUAL in addtion to FASTA

1

Is there currently plans to add functionality to output FASTQ or QUAL files in addition to the FASTA output? I'm curious about this as it would be very useful to...

medcelerate

https://github.com/alyssafrazee/polyester/blob/29263d1a15ee7e33adef5d2d6aeeb93a6cb73d92/R/simulate_experiment.R#L135-L149 > A fold change of X in matrix entry i,j means that for **replicate** j, the baseline mean number of reads (reads_per_transcript[i]) will be multiplied by X. should probably...

ning-y

what I did: ``` simulate_experiment_countmat(fasta = "~/doc/reference/fa/gencode.v32.transcripts.fa", readmat = merges, outdir = "~/tmp/polyester/") ``` the error: ``` Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting...

mhjiang97

read starting position and CIGAR

3

It would be very useful to also get the (ground truth) starting position and CIGAR of each simulated read (when reads are simulated from a GTF and a genome fasta...

esterpantaleo