Analysing MACE-Seq data

Question

[Chris.Vogeley]

Hello everybody,

I have a very fundamental question. For fast transcript-level analysis I use the quasi-mapping-based mode of the salmon tool. For cost reduction we are going to switch to massive amplification of cDNA ends (MACE)- Seq using an Illuminda MiSeq. Do you have any experience if I can run quasi-mapping on MACE-Seq data sets or what do I have to consider for the analysis.

Best regards Chris