Towards progress in batch effects and biases in single-cell RNA-Seq data Stephanie Hicks Dana-Farber Cancer Institute / Harvard SPH @stephaniehicks Single Cell Genomics 2016 Wellcome Genome Campus
Use FASTQ header as a surrogate for batch http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/ swSEQ_mCA_FASTQFiles.htm