reference-point setting from computeMatrix

Question

[QX]

Hi all,

I am looking at the deeptools computeMatrix function:

$ computeMatrix reference-point \ # choose the mode
       --referencePoint TSS \ # alternatives: TES, center
       -b 3000 -a 10000 \ # define the region you are interested in
       -R testFiles/genes.bed \
       -S testFiles/log2ratio_H3K4Me3_chr19.bw  \
       --skipZeros \
       -o matrix1_H3K4me3_l2r_TSS.gz \ # to be used with plotHeatmap and plotProfile
       --outFileSortedRegions regions1_H3K4me3_l2r_genes.bed

For testFiles/genes.bed, with setting for TSS, should I the choose the bed file for gene that contain the peaks or the bed file for the peaks themself? For e.g:

bedfile for peaks:

                      chr     start       end     SYMBOL                 peaks
17:76635401-76637822   17  76635401  76637822 ST6GALNAC1  17:76635401-76637822
19:50010568-50012270   19  50010568  50012270       VRK3  19:50010568-50012270

bedfile for gene contain peaks:

                      chr geneStart   geneEnd     SYMBOL
17:76635401-76637822   17  76629395  76643660 ST6GALNAC1
19:50010568-50012270   19  49994863  50020647       VRK3