slides.md

ChromeQC

author: S. Jackman, J. Chu, E. Erhan, N. Keivanfar, S. La, S. Menon, T. Mozgacheva, B. Orabi, C. Yang, H. Younesy date: 2017-10-22 autosize: true

Summarize sequencing library quality of 10x Genomics Chromium linked reads

Inspiration

Loupe from 10x Genomics

• Reports inferred DNA molecule sizes
• Number of barcodes (GEMs)
• Number of molecules per barcode

Some Loupe Stats

Input DNA Stats	Barcode Stats

Inspiration

FastQC & MultiQC:

• FastQC: Reports base qualities, sequence distribution, GC content, etc
• MultiQC: Aggregate multiple FastQC reports

MultiQC Example

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ChromeQC Pipeline

Pipeline: Subsample

• From subset of fastq files, and subset of read pairs
• Randomly select 4000 out of ~4M whitelisted barcodes
• Extract reads with selected barcodes for downstream analysis
• Report histrograms of unmatched and of whitelisted barcodes

Pipeline: Read Alignment

• minimap
• GRCh38 reference genome
• Group by barcode, sort by position

Pipeline: Molecule Size Extraction

Heuristic:

Any two reads < 60Kbp away are in the same molecule

• Any reads with same position and orientation are discarded except for one

Slide With Plot