Question: Removal of ERCC spike-in in RNA-Seq
gravatar for anu014
10 days ago by
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
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 708 users visited in the last hour