Hi I now analyzing my RNA-Seq data (illumina, 50bp paired end) using CLC Genomics Workbench to verify the results of Galaxy. But now I encounter a problem: should I merge all these files into one before I can carry out downstream analysis or I don't need to do this and the CLC Genomics Workbench can do this? I have RNA-Seq data (paired end) from 4 groups, each group has 6-7 samples (biological replicates). Each sample was sequenced in several lanes and in each lane produced several RNA-Seq files for each sample. The sequencing technician provided many RNA-Seq files for each sample. I know I can merge several data files into one in Galaxy, But can anyone can tell me what should I do in CLC Genomics Workbench for further analysis. Any help would be appreciated.
Dr. Zhang
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