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

Total reads and total mass include ERCC reads and ERCC mass. The ERCC reads and total reads are all displayed in "Details" tab 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.

How does a user view the raw data about the ERCC results?

Please ask IDseq support for the 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 total_ercc_reads.