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.