How to know if an SRA data contains ERCC spike-in?

Question

[Arindam Ghosh]

I am trying to develop an RNA-seq data analysis pipeline. I am following Griffith Lab Tutorial. In the tutorial, the samples contained an additional ERCC. However for the samples that I have downloaded from SRA doesn't contain any. Neither do the Reference Genome downloaded from Ensembl. I have checked about the importance of the use of ERCC. Do all samples generated contain them? While downloading how do I know it it has one?

Answer 1

[Devon Ryan]

Most samples do not contain spike-ins. If spike-ins aren't mentioned in the meta data associated with a sample then said sample likely lacks spike-ins. However, it's not uncommon for this information to simply not be included, so mapping a million or so reads to the ERCC sequences can quickly give you an idea of whether a given sample really has spike-ins or not. Baring further information, that's the only real way to be sure.

[Arindam Ghosh]

In that case are they really important to be considered? Can I collect and analyse data baring ERCC?

[Devon Ryan]

No, they're typically not important and you can normally just ignore them.

[Arindam Ghosh]

Thank you. That brings to a conclusion.