Component: SISSRs

SISSRs

SISSRs is a software application for precise identification of genome-wide transcription factor binding sites from ChIP-Seq data. It is essentially a perl implementation of the SISSRs algorithm outlined in Jothi et al [1], with several new features that were not fully described in the original paper. [1] Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research (2008) 36(16):5221-31.

The component installation folder contains a PDF version of the original manual.

Version	1.0
Bundle	sequencing
Categories
Authors	Lauri Lyly (lauri.lyly@helsinki.fi)
Issue tracker	View/Report issues
Source files	component.xml sissr.sh
Usage	Example with default values SISSRs( treatment = BED, //control = BED, //exclude = TextFile, background_sites = 10, fdr = 0.001, fraglen = -1, genome_size = 2700000000, keep_monostrand_sites = false, keep_single = false, mappable_fraction = 0.8, maxlen = 500, merge_regions = false, min_reads = 2, p_value = 0.001, print_progress = true, report_narrow = false, report_wide = false, window_size = 20 )

Version

1.0

Bundle

sequencing

Categories

Authors

Lauri Lyly (lauri.lyly@helsinki.fi)

Issue tracker

View/Report issues

Source files

component.xml sissr.sh

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
treatment	BED	Mandatory	The aligned ChIP-Seq reads for the sample in BED format.
control	BED	Optional	The aligned ChIP-Seq reads for the control in BED format. [-b ] background file containing tags in BED format to be used as control; -e and -p can be set to desired values to control specificity and specificity, resp.
exclude	TextFile	Optional	[-q ] file containing genomic regions to exclude; reads mapped to these regions will be ignored; file format: 'chr startCoord endCoord'

Name

Type

Mandatory

Description

treatment

BED

Mandatory

The aligned ChIP-Seq reads for the sample in BED format.

control

BED

Optional

The aligned ChIP-Seq reads for the control in BED format. [-b ] background file containing tags in BED format to be used as control; -e and -p can be set to desired values to control specificity and specificity, resp.

exclude

TextFile

Optional

[-q ] file containing genomic regions to exclude; reads mapped to these regions will be ignored; file format: 'chr startCoord endCoord'

Name	Type	Description
output	TextFile	Output file

Name

Type

Description

output

TextFile

Output file

Parameters

Name	Type	Default	Description
background_sites	float	10	[-e] e-value (>=0); it is the number of binding sites one might expect to infer by chance (default: 10); this option is irrelevant if -b option is NOT used
fdr	float	0.001	[-D] false discovery rate (default: 0.001) if random background model based on Poisson probabilities need to be used as control (also check option -b below)
fraglen	int	-1	[-F] average length of DNA fragments that were sequenced (default: estimated from reads, i.e. -1)
genome_size	float	2700000000	Genome size.
keep_monostrand_sites	boolean	false	[-u] (also) reports binding sites supported only by reads mapped to either sense or anti-sense strand; this option will recover binding sites whose sense or anti-sense reads were not mapped for some reason (e.g., falls in unmappable/repetitive regions)
keep_single	boolean	false	[-a] only one read is kept if multiple reads align to the same genomic coordinate (minimizes amplification bias)
mappable_fraction	float	0.8	[-m] fraction of genome mappable by reads (default: 0.8 for hg18, assuming ELAND was used to map the reads; could be different for different organisms and other alignment algorithms)
maxlen	int	500	[-L] upper-bound on the DNA fragment length (default: 500)
merge_regions	boolean	false	[-c] same as the -r (report_region) option, except that it reports binding sites that are clustered within F bp of each other as a single binding region; this is the default option
min_reads	int	2	[-E] min number of 'directional' reads required on each side of the inferred binding site (>0); (default: 2)
p_value	float	0.001	[-p] p-value threshold for fold enrichment of ChIP tags at a binding site location compared to that at the same location in the control data (default: 0.001); this option is irrelevant if -b option is NOT used
print_progress	boolean	true	[-x] do not print progress report (default: prints report)
report_narrow	boolean	false	[-t] reports each binding site as a single genomic coordinate (transition point t in Fig 1A)
report_wide	boolean	false	[-r] reports each binding site as an X-bp binding region centered on inferred binding coordinate; X denotes the distance from the start of the right-most red bar (see Fig 1A in the manuscript; lower-left) to the end of the left-most blue bar surrounding the actual binding site (transition point t in Fig 1A)
window_size	int	20	[-w] scanning window size (even number > 1), which controls for noise (default: 20)

Name

Type

Default

Description

background_sites

float

[-e] e-value (>=0); it is the number of binding sites one might expect to infer by chance (default: 10); this option is irrelevant if -b option is NOT used

fdr

float

0.001

[-D] false discovery rate (default: 0.001) if random background model based on Poisson probabilities need to be used as control (also check option -b below)

fraglen

int

-1

[-F] average length of DNA fragments that were sequenced (default: estimated from reads, i.e. -1)

genome_size

float

2700000000

Genome size.

keep_monostrand_sites

boolean

false

[-u] (also) reports binding sites supported only by reads mapped to either sense or anti-sense strand; this option will recover binding sites whose sense or anti-sense reads were not mapped for some reason (e.g., falls in unmappable/repetitive regions)

keep_single

boolean

false

[-a] only one read is kept if multiple reads align to the same genomic coordinate (minimizes amplification bias)

mappable_fraction

float

0.8

[-m] fraction of genome mappable by reads (default: 0.8 for hg18, assuming ELAND was used to map the reads; could be different for different organisms and other alignment algorithms)

maxlen

int

500

[-L] upper-bound on the DNA fragment length (default: 500)

merge_regions

boolean

false

[-c] same as the -r (report_region) option, except that it reports binding sites that are clustered within F bp of each other as a single binding region; this is the default option

min_reads

int

[-E] min number of 'directional' reads required on each side of the inferred binding site (>0); (default: 2)

p_value

float

0.001

[-p] p-value threshold for fold enrichment of ChIP tags at a binding site location compared to that at the same location in the control data (default: 0.001); this option is irrelevant if -b option is NOT used

print_progress

boolean

true

[-x] do not print progress report (default: prints report)

report_narrow

boolean

false

[-t] reports each binding site as a single genomic coordinate (transition point t in Fig 1A)

report_wide

boolean

false

[-r] reports each binding site as an X-bp binding region centered on inferred binding coordinate; X denotes the distance from the start of the right-most red bar (see Fig 1A in the manuscript; lower-left) to the end of the left-most blue bar surrounding the actual binding site (transition point t in Fig 1A)

window_size

int

[-w] scanning window size (even number > 1), which controls for noise (default: 20)

Anduril

SISSRs

Inputs

Outputs

Parameters