Guide Counting

Now that we have prepared our reference library we are ready to map our records with sgcount.

Running sgcount

sgcount \
  -l uniq.fa \
  -i sample_a.fq.gz sample_b.fq.gz sample_c.fq.gz sample_d.fq.gz \
  -n a b c d \
  -t 4 \
  -g g2s.txt \
  -o mapping.tab

In the above command we are:

  • providing our reference library (uniq.fa or uniq.var.fa) generated previously.
  • providing our fastq files representing our sgrna library to the -i flag,
  • providing an optional custom renaming of those files with the -n flag,
  • stating we will be using 4 threads with the -t flag,
  • providing our gene to sgrna mapping with the -g flag,
  • and writing our results to the output file mapping.tab with the -o flag.

Thats it! Once it finishes we're done with this step.

More information

For more detailed information on optional arguments to this check out the sgcount documentation or for information on how it works at sgcount implementation