Commands

fluff heatmap

fluff heatmap -f <BED> -d <BAM> <BAM> -o <NAME>

Options

Required arguments

  • -f FILE

This need to be a BED file containing features. BED-fomatted files need to contain at least three tab-seperated columns describing chromosome name, start and end.

  • -d [FILE [FILE ...]]

This option is for the data files. They can be aligned sequence data in BAM, BED, wig, bigWig, bedGraph, as well as tabix-indexed format.

  • -o name

This option defines the name of the output files (type determined by extension)

Clustering

  • -C METHOD

By default, fluff heatmap will preserve the order of the features in the input BED file. This is equivalent to specifying -C none. Alternatively, one of two basic clustering methods can be specified using the -C parameter: hierarchical and kmeans. If kmeans is selected the number of clusters (-k) is mandatory.

  • -k INT

Select the number of clusters (Mandatory with kmeans clustering)

  • -M METHOD

There are two options for distance metrics. Euclidean or Pearson (default: Euclidean)

  • -g

Identify dynamics between different time points or conditions. This should be used with Pearson correlation coefficient as distance metric

  • -p PICK

Pick specific data file(s) to use for clustering. You can select using its position e.g -p 1 for first file or -p1,3 for first and third files.

Data processing

  • -r

normalize using RPKM instead of read counts

  • -e INT

extend (in bp. Default: 5000)

  • -b INT

bin size (default 100)

  • -F FRAGMENTSIZE

Fragment length (default: read length)

  • -D

keep duplicate reads (removed by default)

  • -R

keep reads with mapq 0 (removed by default)

  • -m

merge mirrored clusters (only with kmeans and without -g option)

  • -s SCALE

scale (absolute or percentage)

Visualization

  • -c NAME(S)

color(s) (name, colorbrewer profile or hex code)

  • -B NAME(S)

background color(s) (name, colorbrewer profile or hex code)

Other

  • -h

show help message

  • -P INT

number of CPUs (default: 4)

fluff bandplot

fluff bandplot -f <BED> -d <BAM> <BAM> -o <NAME>

Options

Required arguments

  • -f FILE

BED file with cluster in 5th column

  • -d [FILE [FILE ...]]

data files (They can be aligned sequence data in BAM, BED, wig, bigWig, bedGraph, as well as tabix-indexed format.)

  • -counts FILE

read counts table (instead of data files)

  • -o name

output file (type determined by extension)

Data processing

  • -r

normalize using RPKM instead of read counts

  • -S

create summary graphs

  • -b INT

number of bins

  • -F FRAGMENTSIZE

fragment length (default: read length)

  • -D

keep duplicate reads (removed by default)

  • -R

keep repeats (removed by default, bwa only)

  • -s GROUPS

scale groups

  • -p INT,INT

range of percentiles (default 50,90)

  • -P INT

Percentile at which to extract score. Value should be in range [0,100] (default 90)

Visualization

  • -c NAME(S)

color(s) (name, colorbrewer profile or hex code)

Other

  • -h

show help message

fluff profile

fluff profile -i <GENOMIC LOCATION> -d <BAM> <BAM> -o <NAME>

Options

Required arguments

  • -i INTERVAL(S)

one or more genomic intervals (chrom:start-end)

  • -d [FILE [FILE ...]]

data files (They can be aligned sequence data in BAM, BED, wig, bigWig, bedGraph, as well as tabix-indexed format.)

  • -o name

output file (type determined by extension)

Data processing

  • -n

normalize to per million mapped reads

  • -a FILE

annotation in BED12 format

  • -t GROUPS

track groups

  • -s GROUPS

scale groups

  • -S SCALE

scale: ‘auto’ (default), ‘off’ or int for each track

  • -f FRAGMENTSIZE

fragment length (default: 200)

  • -D

keep duplicate reads (removed by default)

  • -R

keep repeats (removed by default, bwa only)

  • -r

reverse

Visualization

  • -c NAME(S)

color(s) (name, colorbrewer profile or hex code)

  • -b BACKGROUND

background color: white | color | stripes

Other

  • -h

show help message