diff --git a/.vscode/settings.json b/.vscode/settings.json index 840f89a..5e5f816 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,7 +1,10 @@ { "cSpell.words": [ + "Nanopore", "chmod", "cygpath", + "demux", + "mkdir", "wphl" ] } \ No newline at end of file diff --git a/ont/README.md b/ont/README.md index c957227..862ee74 100644 --- a/ont/README.md +++ b/ont/README.md @@ -8,7 +8,7 @@ Note that at the time of writing, the GridION runs Ubuntu 16.04 LTS, and mounts ### `ont-demux` ```bash -$ ont-demux FAP_FOLDER +ont-demux FAP_FOLDER ``` Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000 reads/file. It is _highly_ recommended to set the "Number of Reads per File" entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same results. @@ -16,7 +16,7 @@ Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder` ### `ont-transfer` ```bash -$ ont-transfer [-s 1|6|12] FAP_FOLDER +ont-transfer [-s 1|6|12] FAP_FOLDER ``` Transfers all of the passing FAST5 and FASTQ files to the first available USB drive, skipping empty barcodes based on the number of the first skip passed through the `-s` parameter, consolidating all files of the same type into one folder for easier sorting and uploading. @@ -32,7 +32,7 @@ Transfers all of the passing FAST5 and FASTQ files to the first available USB dr See ONT for guppy installation instructions. Others may be installed by opening a terminal and running ```bash -$ sudo apt-get install git parallel -y +sudo apt-get install git parallel -y ``` ### Instructions