Analysis

Standard Analysis

Files provided with different standard analysis at McDermott center Bioinformatics Lab:

RNA sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files (bam format)
  4. Alignment report
  5. Normalized bigwig files (coverage files)
  6. Clustering, dendrogram, report
  7. MDS plot, MA plot, Volcano plot
  8. EdgeR output differential expression files

ChiP Sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files
  4. Normalized wiggle and bigwig files
  5. ChIP-Seq quality measures (phantompeakqualtools)
  6. HOMER generated analysis output files
  7. MACS2 generated peak files
  8. Peak annotated files

Exome Sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files
  4. Mapping statistics
  5. PICARD metrics
  6. Coverage statistics (plots, target region coverage, mean coverage, etc.)
  7. Annotated Variant calls in VCF formats and tab delimited format