I am hoping to use DESeq2 to analyse data from an CaptureSeq data, alongside some RNA Seq data. I can't find anything which discusses the use of DESeq2 for CaptureSeq data analysis. I wondered whether the targeting of specific transcripts in CaptureSeq would alter the distribution of transcript abundances such that my usual DESeq2 pipeline would be invalid? If not, is there anything more complex than limma removeBatchEffect needed to remove the variation between the two techniques?

I realise this is quite a vague question but would appreciate any thoughts anyone has, or pointing in the direction of anyone who has done this previously?

I'm not very familiar with the experiment. Maybe check the papers that consider statistical modeling of the data to see what others have done so far. Sometimes it's fairly easy to plug data into the NB / log linear methods in Bioconductor, with minor tweaks like size factor estimation.