This only applies to aliquots with at least one set of paired-end reads.
Quality assessment is performed pre-alignment with FASTQC and post-alignment with Picard Tools.įiles that were processed after Data Release 14 have associated transcriptomic and chimeric alignments in addition to the genomic alignment detailed above. This workflow outputs a genomic BAM file, which contains both aligned and unaligned reads. Following the methods used by the International Cancer Genome Consortium ICGC ( github), the two-pass method includes a splice junction detection step, which is used to generate the final alignment. STAR aligns each read group separately and then merges the resulting alignments into one. The mRNA Analysis pipeline begins with the Alignment Workflow, which is performed using a two-pass method with STAR. Data Processing Steps RNA-Seq Alignment Workflow To facilitate harmonization across samples, all RNA-Seq reads are treated as unstranded during analyses. These values are generated through this pipeline by first aligning reads to the GRCh38 reference genome and then by quantifying the mapped reads. The GDC mRNA quantification analysis pipeline measures gene level expression in HT-Seq raw read count, Fragments per Kilobase of transcript per Million mapped reads (FPKM), and FPKM-UQ (upper quartile normalization).
#Illumina raw geneious tutorial pdf#