Question: Removal of ERCC spike-in in RNA-Seq
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gravatar for anu014
10 days ago by
anu014140
India
anu014140 wrote:

Hello Biostars!

Can anyone tell me if is it necessary to remove spike-in sequences before aligning FASTQs to reference FASTA OR is it necessary to consider spike-in while normalizing in DEseq2 ? And if yes, how to handle spike-in in RNA-Seq? Can STAR or DEseq handle it somehow?

Please suggest me. Thank you :)

rna-seq alignment assembly • 72 views
ADD COMMENTlink modified 10 days ago by Devon Ryan79k • written 10 days ago by anu014140
1
gravatar for Devon Ryan
10 days ago by
Devon Ryan79k
Freiburg, Germany
Devon Ryan79k wrote:

Presuming you mean ERCC spike-ins the best practice is to include them in the reference genome. However in practice not doing so has little if any effect, so we rarely bother. Unless you have a use-case that absolutely requires spike-ins, it's best to simply ignore them (i.e., do not use them in any way in your analysis).

ADD COMMENTlink written 10 days ago by Devon Ryan79k
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