Command Line Utilites¶
Convert BAM to BED¶
usage: bam2bed [-h] [-b BFILE] [-l LTYPE] [-lower LOWER] [-upper UPPER]
[-e EXTEN] [-t FILETYPE] [-o OFILE]
Transform BAM reads to resemble the true position of a ChIP seq fragment.
optional arguments:
-h, --help show this help message and exit
-b BFILE BAM file. Aligned single or paried-end ChIP-seq reads
-l LTYPE INT. Library type: 0 if library is paired-end, fragment length
is estimated from data; different from 0 if library is single-
end, the value assigned here is used as fragment length.
-lower LOWER INT. Lower isize of paired-end read. Default: 0
-upper UPPER INT. Upper isize of paired-end read. Default: 200
-e EXTEN INT. Half length of each read around their fragment midpoing.
-t FILETYPE STR. Type of output file: 'bam' or 'bed'. If chosen 'bam', and
optional field, 'AL:i', is added containg the average length
of the fragments.
-o OFILE Output file.
Counts the number of overlapping between two BED files¶
None
usage: checkMatches [-h] [-f1 FILE1] [-f2 FILE2] [-o OFILE]
Counts the number of overlapping between two BED files.
optional arguments:
-h, --help show this help message and exit
-f1 FILE1 BED enrichment file replicate 1.
-f2 FILE2 BED enrichment file replicate 2.
-o OFILE BED enrichment file with the intersection of replicates 1 and 2.
Generate coverage over nucleosomes¶
None
usage: getAvrCov [-h] [-b BFILE] [-n NFILE] [-f FSIZE] [-w WWIDTH] [-o OFILE]
Generate coverage over nucleosomes.
optional arguments:
-h, --help show this help message and exit
-b BFILE BAM file.
-n NFILE BED file with enriched nucleosomes.
-f FSIZE INT. Fragment size of the reads.
-w WWIDTH INT. Half width of plotting window.
-o OFILE Prefix of output files.
Count reads per nucleosome¶
None
usage: getCounts [-h] [-b BFILE] [-t FILETYPE] [-n NFILE] [-pValue PVALUE]
[-upper UPPER] [-lower LOWER] [-l LTYPE] [-e EXTEN]
[-o OFILE]
Count reads per nucleosome.
optional arguments:
-h, --help show this help message and exit
-b BFILE BAM or BED file. ChIP-seq reads.
-t FILETYPE STR. File type: bed or bam. Default: bam.
-n NFILE BED file. Nucleosome position data, output of Danpos or
iNPS.
-pValue PVALUE FLOAT file. -log of pValue cut-off of nucleosomes on BED
file.
-upper UPPER INT. Upper threshold for insert size. Default: 200. Not used
if fileType is bed
-lower LOWER INT. Lower threshold for insert size. Default: 0. Not used
if fileType is bed
-l LTYPE INT. Library type: if equal to 0, data is assumed to be
paired-end and read lengths are estimated from data itself;
if different from 0, data is assumed to be single-end and
read lengths use this value extend every read. Not used if
fileType is bed
-e EXTEN INT. Half length of reads extended at their midpoint.
-o OFILE STR. Name of output file.
Produces coverage figures¶
None
usage: getFigures [-h] [-b BFILE] [-n NFILE] [-f FRAGL] [-hr HALFR]
[-hw HALFW] [-o OFILE]
Generate coverage figures.
optional arguments:
-h, --help show this help message and exit
-b BFILE BAM file.
-n NFILE BED file with nucleosome positions.
-f FRAGL Fragment length if single-end library. If library is paired-end,
provide 0 as fragment length.
-hr HALFR Half length of reads extended at their midpoint.
-hw HALFW Half length of the windows.
-o OFILE Output file.
Generate coverage over nucleosomes¶
None
usage: getProfile [-h] [-c CONFFILE] [-d DATABASE] [-w WWIDTH] [-lower LOWER]
[-upper UPPER] [-perc PERC] [-plotNucs PLOTNUCS]
[-localMaxFile LOCALMAXFILE] [-clustering CLUSTERING]
[-t TITLE] [-fs FSIZE] [-kc KCLUSTERS] [-kp KPOINTS]
[-cols COLS] [-o PREFIX]
Generate coverage plots.
optional arguments:
-h, --help show this help message and exit
-c CONFFILE STR. Name of configuration file.
-d DATABASE STR. Name of database with TSS info.
-w WWIDTH INT. Half width of plotting window.
-lower LOWER INT or colon separated list of INT. Lower insert size
to be considered. Default: 0
-upper UPPER INT. Upper insert size to be considered. Deafult: 200
-perc PERC FLOAT. Percentile of top extreme values to be
discarded.
-plotNucs PLOTNUCS STR. Plot nucleosome positions: 'true' or 'false'.
Default = 'false'.
-localMaxFile LOCALMAXFILE
STR. File containing positions of nucleosomes relative
to TSS. Default = 'none'.
-clustering CLUSTERING
STR. Either kmeans or none.
-t TITLE STR. Title of output figure.
-fs FSIZE INT. Font size.
-kc KCLUSTERS INT. Number of clusters for heatmap's k-means
clustering.
-kp KPOINTS INT. Number of points to be used on heatmap's during
k-means clustering.
-cols COLS INT. Number of columns for the heatmap.
-o PREFIX Prefix of output files.
Meges the rows of two BED files¶
None
usage: merged [-h] [-f1 F1FILE] [-f2 F2FILE] [-o OFILE]
Merge the rows of two BED files.
optional arguments:
-h, --help show this help message and exit
-f1 F1FILE BED file. File 1.
-f2 F2FILE BED file. File 2.
-o OFILE STR. Name of output file.
Creates bedGraph file with the enriched regions given a signal and control, and expected counts files¶
None
usage: getEnrichedRegions [-h] [-signal SIGNAL] [-control CONTROL]
[-expV EXPV] [-marker MARKER] [-writeAll WRITEALL]
[-prefix PREFIX]
Creates bedGraph file with the enriched regions given a signal and control,
and expected counts files.
optional arguments:
-h, --help show this help message and exit
-signal SIGNAL BED file. Signal counts.
-control CONTROL BED file. Control counts.
-expV EXPV TXT file. Expected counts.
-marker MARKER INT. Value to put next to enriched nucleosomes. Default
1000.
-writeAll WRITEALL Bool. If 'true' write all nucleosomes with a 1 for
enriched nucleosomes and 0 otherwise. If 'false' only
print enriched nucleosomes. Default 'false'
-prefix PREFIX STR. Prefix of output file.