These two options can be used to fine-tune the peak calling behavior by specifying the minimum length of a called peak and the maximum allowed gap between two nearby regions to be merged. In another word, a called peak has to be longer than *min-length*, and if the distance between two nearby peaks is smaller than *max-gap* then they will be merged as one. If they are not set, MACS2 will set the DEFAULT value for *min-length* as the predicted fragment size d, and the DEFAULT value for *max-gap* as the detected read length. Note, if you set a *min-length* value smaller than the fragment size, it may have NO effect on the result. For BROAD peak calling, try to set a
large value such as 500bps. You can also use '--cutoff-analysis' option with default setting, and check the column 'avelpeak' under different cutoff values to decide a reasonable *min-length* value.
These two options can be used to fine-tune the peak calling behavior
by specifying the minimum length of a called peak and the maximum
allowed gap between two nearby regions to be merged. In another word,
a called peak has to be longer than *min-length*, and if the distance
between two nearby peaks is smaller than *max-gap* then they will be
merged as one. If they are not set, MACS2 will set the DEFAULT value
for *min-length* as the predicted fragment size d, and the DEFAULT
value for *max-gap* as the detected read length. Note, if you set a
*min-length* value smaller than the fragment size, it may have NO
effect on the result. For BROAD peak calling, try to set a large value
such as 500bps. You can also use '--cutoff-analysis' option with
default setting, and check the column 'avelpeak' under different
cutoff values to decide a reasonable *min-length* value.
- fold enrichment for this peak summit against random Poisson distribution with local lambda,
- -log10(qvalue) at peak summit
Coordinates in XLS is 1-based which is different with BED format. When `--broad` is enabled for broad peak calling, the pileup, pvalue, qvalue, and fold change in the XLS file will be the mean value across the entire peak region, since peak summit won't be called in broad peak calling mode.
Coordinates in XLS is 1-based which is different with BED
format. When `--broad` is enabled for broad peak calling, the
pileup, pvalue, qvalue, and fold change in the XLS file will be the
mean value across the entire peak region, since peak summit won't
be called in broad peak calling mode.
2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the
peak locations together with peak summit, pvalue and qvalue. You
can load it to UCSC genome browser. Definition of some specific
columns are:
- 5th: integer score for display. It's calculated as `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on whether `-p` (pvalue) or `-q` (qvalue) is used as score cutoff. Please note that currently this value might be out of the [0-1000] range defined in [UCSC Encode narrowPeak format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by using the following 1-liner awk: `awk -v OFS="\t" '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`
- 5th: integer score for display. It's calculated as
`int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on
whether `-p` (pvalue) or `-q` (qvalue) is used as score
cutoff. Please note that currently this value might be out of the
[0-1000] range defined in [UCSC Encode narrowPeak
format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You
can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by
