Question: Removal of ERCC spike-in in RNA-Seq
0
gravatar for anu014
3 months ago by
anu014150
India
anu014150 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 • 197 views
ADD COMMENTlink modified 3 months ago by Devon Ryan82k • written 3 months ago by anu014150
1
gravatar for Devon Ryan
3 months ago by
Devon Ryan82k
Freiburg, Germany
Devon Ryan82k 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 3 months ago by Devon Ryan82k

Hi @Devon . What if the data is single cell RNA-seq?

ADD REPLYlink written 11 weeks ago by anu014150
1

scRNA-seq can sometimes benefit from spike-ins. Just align to them and use them for computing scaling factors.

ADD REPLYlink written 11 weeks ago by Devon Ryan82k
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