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Bioinformatic Analysis – FAQs

  1. What does the core package include for analysis? Data generated from the core will be processed through the standard Cell Ranger pipeline (10X Genomics). Raw data, QC metric data, count matrices, and browsable data files in Loupe Cell format will be made available to investigators.
  2. What are the steps taken for QC? The Cell Ranger pipeline performs initial QC and provides a matrix with counts per GEMs that are likely cells (A link to the cell calling algorithm by Cell Ranger can be found here). We recommend performing extra-downstream filters based on number of genes per cell and mitochondrial content (appropriate thresholds may vary per experimental design and cell type).
  3. How much time will it take to get my data? The timeline will be based on sample numbers and the scheduling queue of the core.
  4. Is there an option for additional analysis beyond what is offered in the package? Unfortunately, at this time, we are unable to provide this service. We hope to soon!
  5. How can I understand the data output and get recommendations of downstream analyses? You can check out our Data Output User Guide, which explains the folder structure of the data, and provides links to tutorials, packages, books and articles that can help you analyze the data.
  6. Are there any groups at BWH that meet to share knowledge and skills in the interdisciplinary field of Bioinformatic Analysis? Yes, the Bioinformatics Club at Brigham & Women’s Hospital meets weekly to provide training and hosts speakers to support advances in this exciting field. If you’d like to join the club, please visit the website here: http://bioinformatics.bwh.harvard.edu/
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