reference-point setting from computeMatrix
0
0
Entering edit mode
9 weeks ago
QX ▴ 60

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
ATACseq • 166 views
ADD COMMENT

Login before adding your answer.

Traffic: 1147 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6