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?
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Arindam Ghosh
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.
In that case are they really important to be considered? Can I collect and analyse data baring ERCC?
No, they're typically not important and you can normally just ignore them.
Thank you. That brings to a conclusion.
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