Entering edit mode
9 weeks ago
QX
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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