Catchitt

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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