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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.