Extract barcode sequences and correct sequencing errors
bxcheck trim -l known-barcodes.txt input.fq.gz -o output
Plot some stats
plot-bxcheck.py output.txt -d fq-plots/
Run stats on mapped 10x BAM, requires BX tags
bxcheck stats -l known-barcodes.txt mapped.bam > stats.txt
Plot the stats
plot-bxcheck.py stats.txt -d bam-plots/
# or
plot-bxcheck.py output.txt stats.txt -d fq-and-bam-plots/
Plot summary stats highlighting differences between multiple samples
cat summary.conf
fSpaAur1 /path/to/fSpaAur1/trim.txt
fSpaAur1 /path/to/fSpaAur1/bxcheck.txt
fCotGob3 /path/to/fCotGob3/trim.txt
fCotGob3 /path/to/fCotGob3/bxcheck.txt
mOncTor1 /path/to/mOncTor1/trim.txt
mOncTor1 /path/to/mOncTor1/bxcheck.txt
fErpCal1 /path/to/fErpCal1/trim.txt
fErpCal1 /path/to/fErpCal1/bxcheck.txt
fAnaTes1 /path/to/fAnaTes1/trim.txt
fAnaTes1 /path/to/fAnaTes1/bxcheck.txt
fMasArm1 /path/to/fMasArm1/trim.txt
fMasArm1 /path/to/fMasArm1/bxcheck.txt
plot-summary.py -i summary.conf summary.html
An example of plot-bxcheck output and plot-summary output.