FAQ

What is FinaleDB?

FinaleDB, FragmentatIoN AnaLysis of cEll-free DNA DataBase, is a comprehensive cell-free DNA (cfDNA) fragmentation pattern database to host uniformly processed and quality controlled 2579 paired-end cfDNA WGS datasets from 2505 samples across 23 different pathological conditions in the existing public domain.

What information is available?

Each entry in the FinaleDB is related to a sequencing run of a given sample. The entry comes with the following information:

• A unique FinaleDB entry ID, which is of the format: EE87282

• SRA ID if the entry corresponds to an item in SRA database

• Number of fragments

• Sequencing configuration, e.g. the read length, sequencing instrument, etc.

• Sample information, including:

  • Sample name

  • Sample type, e.g. plasma, urine, culture medium, etc.

  • Pathological condition

  • Age and gender of the subject

• Publications of the corresponding study.

• Quality control data, including:

  • FASTQC files

  • A comprehensive MultiQC report

• Overal metrics

  • Picard library complexity

  • Picard GC bias analysis

  • Fragment statistics

• Fragmentation pattern data:

  • Fragment size distribution

  • Fragment size profile

  • Fragment coverage profile

  • Windowed-Protection Score (WPS)

Notice that some entries may contain only some of the above information.

What data files can I download?

FinaleDB provides the following data files for download:

• Quality control

• Fragment size distribution

• Fragmentation data files (tab-separated values format)

• Fragment size profile (bedGraph)

• Fragment coverage profile (bedGraph)

• WPS track (bedGraph)

You need to add the entries to the download list either at the query page, or the visualization page, and then go to the download center to start downloading. Notice that all the files will be downloaded separately.

Can I have programmatic access?

FinaleDB comes along with a set of RESTful APIs. Please refer to the API reference for more details:

API Reference

I found missing or incorrect information. What should I do?

Please contact Yaping Liu (yaping.liu at cchmc.org) or Haizi Zheng (haizi.zheng at cchmc.org).

I want to make contributions. How to submit new data?

That's wonderful! Contributions from the community are always welcome! Since FinaleDB is a comprehensive manually-curated database, please contact us at Yaping Liu (yaping.liu at cchmc.org) or Haizi Zheng (haizi.zheng at cchmc.org).