ERCC Counts Information

The total input RNA (in picograms) for a sample can be estimated using ERCC spike-ins by:

total_pg = ercc_pg / ercc_reads * total_reads

The ERCC reads and total reads are all displayed in the browser. Total reads can also be obtained from the project sample_table.csv. If you need to programatically obtain the ERCC reads, they can be gotten from the reads_per_gene.star.tab results file as follows:

grep "^ERCC" reads_per_gene.star.tab | awk '{sum += $2} END {print 2*sum}'

That is, filter to all rows starting with "ERCC", sum the second column, then multiply by 2.