Someone wrote this manual for my small bcsplit script. I justed merged into my readme. Thanks, stranger :-)
I saw someone on the Nanopore community unsure of how to use the program so these are some install steps that I used. Until guppy
can demultiplex files natively (which should be soon), other programs will have to be used. If you've already run guppy_barcoder
this script will work for you. Thanks to Michael Schmid for making the script.
biopython
is required for guppy_bcsplit
as it imports the Bio
module from SeqIO
in biopython
to function. guppy_bcsplit
works in python 2.7
and python 3.7.1
for me.
Clone the git repository:
git clone https://github.com/ms-gx/guppy_bcsplit.git
It's only one python file so you could easily put it anywhere.
Unless you change your PATH you'll have to cd
and execute the script where it's located with ./guppy_bcsplit.py
:
If you have multiple fastq files, you'll need to concatenate them first:
cat source_folder/*.fastq >> destination_folder/name.fastq
Unless you've added guppy_bcsplit to PATH you will need cd
and run it from the folder with ./guppy_bcsplit.py
The following commands for guppy_bcsplit are:
-b
is the folder containing the guppy barcoding summary file generated by guppy
.
-f
is the folder containing the .fastq
files. If you wanted to point to a specific file, just add name .fastq
after the folder
-p
is the prefix that gets attached to barcodeXX
so it will look like prefix_barcodexx.fastq
.
-s
is the folder where guppy_bcsplit will output a summary text of how many of each barcodes and unclassified reads there were.
./guppy_bcsplit.py -b folder_containing_guppy_barcode_summary/barcoding_summary.txt -f folder_containing_guppy_fastq_concatenated/ -p prefix -s folder/guppy_bcsplit_summary.txt
guppy_bcsplit
should now demultiplex your barcodes and unclassified reads to separate .fastq
files and create a summary output.