Bartender¶
Bartender converts sequence data to a frequency table containing discovered barcode and raw reads count.
Bartender is available as a module on Apocrita.
Usage¶
To run the default installed version of Bartender, simply load the bartender
module:
module load bartender
For usage documentation, run pass the -h switch to any of the Bartender
python scripts, for example: bartender_combiner_com -h.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 2GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bartender
# Test extractor using example barcode pattern
bartender_extractor_com -f example.fq \
-o example \
-p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA
# Group barcodes using the clustering component
bartender_single_com -f example_barcode.txt \
-o example \
-t ${NSLOTS}