Tab

Method

Option

Value

General

N/A

Mer Length

15

Create a file of unassigned sequences for each sample

unchecked

Create graphs

unchecked

Create alignment files

unchecked

Peak Detection

QSeq Peak Finder (default)

Minimum number of reads (RPM)

4

Maximum distance between reads

50

Minimum fold enrichment

4

Minimum peak height (RPM)

0.5

Shift reads

unchecked

Number of bases

default if Shift reads is checked; 0

Use directionality

ChIP-Seq: checked

miRNA: unchecked

Fraction of + reads on left side

0.4

Minimum fraction of + reads

0.25

Maximum fraction of + reads

0.75

Trim peak signals

ChIP-Seq data: checked, 10%

miRNA: unchecked

Trim %

10

Tag Size

Calculate tag size is selected; value is the average read length

Use reads that map to multiple locations

checked

Simple Peak Finder

Minimum number of reads within the region

If no control lane: 20

If control lane: 8

Maximum distance between reads in the region

75

Minimum fold enrichment over the control

5

Automatically calculate tag size

checked

Tag size

25

MACS Peak Detection

Automatically calculate genome size

checked

Genome size

2700000000

Automatically calculate tag size

checked

Tag size

25

PValue cutoff

0.00001

MFold

32

Build a shifting model

checked

Shift size

100

Bandwidth

300

Lambda

checked

Lambda set

1000, 5000, 10000

Sequence Handling

N/A

Require at least ‘x’ bases

20

… and at least ‘x’ % of the bases matching within each read

80

Exclude bases before position

unchecked; if checked, default is ‘1’

Exclude bases after position

unchecked; if checked, default is ‘1000’

Maximum allowed gap shift

available only for Custom read technology; default is 3

Single

available only for Custom read technology; default is 10

Accumulated per read

available only for Custom read technology; default is 30

Other/Internal

N/A

Filter out reads that match more than ‘x’ place(s) equally

checked; 25

Automatically determine mer repeat settings

checked

Filter out mers that occur more than ‘x’ time(s)

available only when Automatically determine mer repeat settings is unchecked; 150

Don’t delete Reference (Template) mer files

unchecked

Don’t delete Sample mer files

unchecked

Don’t delete hit files

unchecked

How should QSeq use the disk while finding matches?

Automatic

Create a profile of the reads in RAM (searches less of the genome)

Automatic: unavailable

All others: checked

Align read sequences to template more precisely (requires more RAM)

checked

Minimize mers (may degrade results)

checked

Minimizer level

2

Target max # of parallel pipelines

checked; if unchecked, the default is equal to the number of cores in the computer (e.g. 4, 8, etc.)