Analyzing data produced by the UMI based SCRB-seq (Soumillon et al. 2014) protocol.

Question

[halo22]

Hello All,

I am working on analyzing single cell RNA-seq data generated using the SCRB-seq protocol. The data that I have has already gone through data pre-processing including demultiplexing the BCL files using Picard, alignment with STAR, QC with RNASeqQC and marking duplicates with UmiAwareMarkDuplicatesWithMateCigar also with Picard. The only sequence files that I have to access to are the BAM files with duplicates marked using Picard. I would like to run RSEM or HT-seq for transcript quantification. Is it a good idea to just remove the Picard marked duplicates and then run RSEM on the data? I appreciate all help and suggestions.