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name |
comment |
type |
|
c |
Conservative peaks (NarrowPeak file containing the conservative peaks) |
FILE |
r |
Relaxed peaks (NarrowPeak file containing the relaxed peaks) |
FILE |
f |
FAI of genome (FastA index file of the genome) |
FILE |
b |
Bin width (The width of the genomic bins considered, valid range = [1, 10000], default = 50) |
INT |
rw |
Region width (The width of the genomic regions considered for overlaps, valid range = [1, 10000], default = 50) |
INT |
outdir |
The output directory, defaults to the current working directory (.) |
STRING |
name |
comment |
type |
|
d |
Data source (The format of the input file containing the coverage information, range={BAM/SAM, Bigwig}, default = BAM/SAM)
Parameters for selection "BAM/SAM": |
i |
Input SAM/BAM (The input file containing the mapped DNase-seq/ATAC-seq reads) |
FILE |
Parameters for selection "Bigwig": |
i |
Input Bigwig (The input file containing the mapped DNase-seq/ATAC-seq reads) |
FILE |
f |
FastA index (The genome index) |
FILE |
| |
b |
Bin width (The width of the genomic bins considered) |
INT |
outdir |
The output directory, defaults to the current working directory (.) |
STRING |
name |
comment |
type |
|
m |
Motif model (The motif model in Dimont, HOCOMOCO, or Jaspar format, range={Dimont, HOCOMOCO, Jaspar}, default = Dimont)
Parameters for selection "Dimont": |
d |
Dimont motif (Dimont motif model description) |
FILE |
Parameters for selection "HOCOMOCO": |
h |
HOCOMOCO PWM (PWM from the HOCOMOCO database) |
FILE |
Parameters for selection "Jaspar": |
j |
Jaspar PFM (PFM in Jaspar format) |
FILE |
| |
g |
Genome (Genome as FastA file) |
FILE |
f |
FAI of genome (FastA index file of the genome) |
FILE |
b |
Bin width (The width of the genomic bins considered) |
INT |
l |
Low-memory mode (Use slower mode with a smaller memory footprint, default = false) |
BOOLEAN |
outdir |
The output directory, defaults to the current working directory (.) |
STRING |
name |
comment |
type |
|
a |
Accessibility (File containing accessibility features) |
FILE |
m |
Motif (File containing motif features) |
FILE |
l |
Labels (File containing the labels) |
FILE |
f |
FAI of genome (FastA index file of the genome) |
FILE |
b |
Bin width (The width of the genomic bins, valid range = [1, 1000], default = 50) |
INT |
n |
Number of bins (The number of adjacent bins, valid range = [1, 20], default = 5) |
INT |
abb |
Aggregation: bins before (The number of bins before the current one considered in the aggregation, valid range = [1, 20], default = 1) |
INT |
aba |
Aggregation: bins after (The number of bins after the current one considered in the aggregation, valid range = [1, 20], default = 4) |
INT |
i |
Iterations (The number of iterations of the interative training, valid range = [1, 20], default = 5) |
INT |
t |
Training chromosomes (Training chromosomes, separated by commas, OPTIONAL) |
STRING |
itc |
Iterative training chromosomes (Chromosomes with predictions in iterative training, separated by commas, OPTIONAL) |
STRING |
p |
Percentile (Percentile of the prediction scores of positives used as threshold in iterative training, valid range = [0.0, 1.0], default = 0.99) |
DOUBLE |
outdir |
The output directory, defaults to the current working directory (.) |
STRING |
name |
comment |
type |
|
c |
Classifiers (The classifiers trained by iterative training) |
FILE |
a |
Accessibility (File containing accessibility features) |
FILE |
m |
Motif (File containing motif features) |
FILE |
f |
FAI of genome (FastA index file of the genome) |
FILE |
p |
Prediction chromosomes (Prediction chromosomes, separated by commas, OPTIONAL) |
STRING |
abb |
Aggregation: bins before (Number of bins before the current one considered for aggregation., OPTIONAL) |
INT |
aba |
Aggregation: bins after (Number of bins after the current one considered for aggregation., OPTIONAL) |
INT |
n |
Number of classifiers (Use only the first k classifiers for predictions., OPTIONAL) |
INT |
outdir |
The output directory, defaults to the current working directory (.) |
STRING |