![]() BAM index file pairing is not supported by this method of sorting, which does not allow for BAM slicing on these alignments. The transcriptomic alignment is also sorted differently to facilitate downstream analyses. The transcriptomic alignment reports aligned reads with transcript coordinates rather than genomic coordinates. The genomic alignment files contain chimeric and unaligned reads to facilitate the retrieval of all original reads. The chimeric BAM file contains reads that were mapped to different chromosomes or strands (fusion alignments). 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 data are generated through this pipeline by first aligning reads to the GRCh38 reference genome and then by quantifying the mapped reads. These values are additionally annotated with the gene symbol and gene bio-type. Subsequently the counts are augmented with several transformations including Fragments per Kilobase of transcript per Million mapped reads (FPKM), upper quartile normalized FPKM (FPKM-UQ), and Transcripts per Million (TPM). The GDC mRNA quantification analysis pipeline measures gene level expression with STAR as raw read counts. fa-file-text Download PDF /Data/PDF/Data_UG.pdf.Bioinformatics Pipeline: Protein Expression.Bioinformatics Pipeline: Methylation Analysis Pipeline.Bioinformatics Pipeline: Copy Number Variation Analysis.Bioinformatics Pipeline: miRNA Analysis.Bioinformatics Pipeline: DNA-Seq Analysis.fa-file-text Download PDF /Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf.Data Transfer Tool Command Line Documentation.fa-file-text Download PDF /Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf.Before Submitting Data to the GDC Portal.fa-file-text Download PDF /Data_Portal/PDF/Data_Portal_UG.pdf.fa-file-text Download PDF /API/PDF/API_UG.pdf.Appendix C: Format of Submission Queries and Responses.
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