Devon O'Rourke

I wonder if I'm making a mess of this because the job is submitted to our cluster through SLURM, and I believe that by passing the `#SBATCH --output` parameter, I'm...

Just tested using the sample data and passing the `#SBATCH --error racon.log` and `#SBATCH --output racon.fasta` commands work as hoped for. Next question is whether or not the script will...

What I can confirm after 5 minutes of the program running is that: 1. A new directory (`racon_work_directory_1536342564.47`) containing two files (`contigs_0.fasta` and `contigs_1.fasta`) has been created. 2. `contigs_0.fasta` and...

Thanks Jon, I'm generating these data in the next couple of weeks. I'll let you know how testing goes soon. I'll send you some test data if you'd like? Devon

I have generated a tiny bit of 16-S data a few months ago; totally failed experiment I was trying as part of a high school 1-week workshop (apparently bad reagents...

Thanks for the reply. **version** ``` Japsa: A Java Package for Statistical Sequence Analysis Version 1.7-05b, Built on Mon Jul 09 15:42:09 EDT 2018 with javac 1.8.0_144 ``` Log file...

One thing to note: the .bam file has `1587` contigs, while the resulting scaffold file that npScarf produced has just 131 unique sequences. Maybe I'm just making an oversight. Is...

Thanks - can we back up a step? Where does npScarf pull the coverage info; could I supply a file that does that into the current command as a parameter?...

install DEseq2 and genefilter from Bioconductor separately before installing btools. https://bioconductor.org/packages/release/bioc/html/DESeq2.html http://bioconductor.org/packages/release/bioc/html/genefilter.html so: ``` BiocManager::install("DESeq2") BiocManager::install("genefilter") ``` then... ``` devtools::install_github('twbattaglia/btools') ```