How do I interpret the quality of my ERCC results?

ERCC Quality Interpretation

The 96 synthetic RNA spike-in developed by the External RNA Controls Consortium (ERCC) can be used to assess experimental variability.

Counts of the ERCC reads and total reads are all displayed in the "Sample Details" tab on the Sample Report page.

In a clean, high-quality sequenced sample, read counts for each ERCC sequence should linearly track their spike-in concentrations.

Total read counts can also be obtained from the project sample_table.csv. If you need to programmatically obtain the ERCC reads, they can be retrieved 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.

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

input_pg = ercc_pg / ercc_reads * (total_reads - total_ercc_reads)

How does a user view the raw data about the ERCC results? Please ask CZ ID support (by clicking "Contact Us" in the drop-down menu in your profile) for the host gene counts for the project. This includes the ERCC information.

What is the best way to get a table of ERCC counts for all samples in a project? ERCC counts are in the project sample table, column ERCC Reads.