How is the mapped fragment number calculated? (Under the Read Statistics tab of the Detailed Summary page)

Read_Statistics

Archer Analysis utilizes BWA and Bowtie 2 for mapping to hg19. Any read that has an Alignment Score less than 30 is removed from consideration. Reads with a mapping quality less than 30 are either multiple mapping reads or contain many low-quality bases (low FASTQ base quality). For the exact calculation of the mapping quality and the factors involved, please refer to the BWA and Bowtie 2 documentation. Note that this default value can be adjusted by the user under Analysis Settings in Archer Analysis.

BWA: http://bio-bwa.sourceforge.net/bwa.shtml

Bowtie: http://bowtie-bio.sourceforge.net/index.shtml


For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.

How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2017 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.