fix description on 5th column of narrowPeak file. Related to
@@ -453,7 +453,7 @@ and peak summit positions.
can load it to UCSC genome browser. Definition of some specific
columns are:
- - 5th: integer score for display calculated as `int(-10*log10qvalue)`. 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)
+ - 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`
- 7th: fold-change
- 8th: -log10pvalue
- 9th: -log10qvalue
@@ -462,12 +462,12 @@ and peak summit positions.
The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to
analyze it by other tools.
-3. `NAME_summits.bed` is in BED format, which contains the peak summits
- locations for every peaks. The 5th column in this file is
- -log10pvalue the same as NAME_peaks.bed. If you want to find the
- motifs at the binding sites, this file is recommended. The file
- can be loaded directly to UCSC genome browser. Remove the
- beginning track line if you want to analyze it by other tools.
+3. `NAME_summits.bed` is in BED format, which contains the peak
+ summits locations for every peaks. The 5th column in this file is
+ the same as NAME_peaks.narrowPeak. If you want to find the motifs
+ at the binding sites, this file is recommended. The file can be
+ loaded directly to UCSC genome browser. Remove the beginning track
+ line if you want to analyze it by other tools.
4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to
narrowPeak file, except for missing the 10th column for annotating
