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)
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)
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