• Principal Investigator:
  • Researcher:
  • Experiment:

bcbio run data was imported from /Users/travis/build/hbc/bcbio_rnaseq_output_example.

Count matrices

## Saving raw_counts.rda, normalized_counts.rda, tpm.rda to /Users/travis/build/hbc/bcbio_rnaseq_output_example/report/data
## Writing raw_counts, normalized_counts, tpm to /Users/travis/build/hbc/bcbio_rnaseq_output_example/report/results/2018-06-18/counts

The results are saved as gzip-compressed comma separated values (CSV). Gzip compression is natively supported on macOS and Linux-based operating systems. If you’re running Windows, we recommend installing 7-Zip. CSV files can be opened in Excel or RStudio.

  • normalized_counts.csv.gz: Use to evaluate individual genes and/or generate plots. These counts are normalized for the variation in sequencing depth across samples.
  • tpm.csv.gz: Transcripts per million, scaled by length and also suitable for plotting.
  • raw_counts.csv.gz: Only use to perform a new differential expression analysis. These counts will vary across samples due to differences in sequencing depth, and have not been normalized. Do not use this file for plotting genes.

Read metrics

Total reads