I realised that the description of how we got from the downloading the reads to pre-processing them and finally getting the counts matrices and logRPKM values is not mentioned anywhere in the package. Can @Malvikakh and @chinweetan work on getting this sorted? This could possibly be included in the object documentation. Please include detailed information on the specific reference genome used and the annotation files used.
I realised that the description of how we got from the downloading the reads to pre-processing them and finally getting the counts matrices and logRPKM values is not mentioned anywhere in the package. Can @Malvikakh and @chinweetan work on getting this sorted? This could possibly be included in the object documentation. Please include detailed information on the specific reference genome used and the annotation files used.