Determine ERCC presence

[earonesty]

My one-liner of the day:

Is there ERCC spiked into my sample?

fastq-mcf n/a -l 30 $fq1 | zhead -n 100000 | bowtie -p 4 -S -m 1 --best --strata  ercc92.fa - 2>&1 > /dev/null | perl -ne '($c)=/Reported (\d+)/; $c+=0; END {print "$c\n"};'

This scans the fastq for reads that are not N's and have OK quality and have a minimum of 30 base pairs. Then it takes the first 100k reads of that sort and sends them to bowtie, which looks for non-ambiguous ERCC hits. ERCC's are alien enough that a count of 2 or more is sufficient for "detection" of ERCC.

This script is very fast (completing in <1 second, 2.474 seconds of CPU time), and informs downstream programs that ERCC is present and should be dealt with appropriately (quantified, reported on, subtracted, etc.)