Question about different information included in the input bed file would generate totally different Metagene Plot

[lillianj97]

Hi,

I use same command to map the location to my methylation data.

computeMatrix scale-regions -p 8 -R Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test.bed -S Res2_MeDIP_Merge.sort.ReDup.bw Res2_Input_Merge.sort.ReDup.bw --beforeRegionStartLength 5000 --regionBodyLength 5000 --afterRegionStartLength 5000 -o Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test_gene.gz --outFileSortedRegions Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test_gene.bed --missingDataAsZero --skipZeros

plotHeatmap -m Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test_gene.gz -out Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test_GeneBody_Heatmap.png --dpi 720 --yMin 0 --yMax 1800

The only different thing is "Short_Up_Group1_Res2_Loci_Methy_Res2Treated_test.bed". I used UCSC "https://genome.ucsc.edu/cgi-bin/hgTables" to generate the bed file of gene location (hg38, gencodeV29).

For Fig1 (peaks enriched closed to the TSS sites), the bed file looks like below:
chr1 148402714 148402875 ENST00000364313.1 0 + 148402714 148402714 0 1 161, 0,
chr1 149636765 149636929 ENST00000384101.1 0 + 149636765 149636765 0 1 164, 0,
chr1 202604267 202605293 ENST00000428573.1 0 + 202604267 202604267 0 2 68,246, 0,780,

For Fig2 (peaks enriched closed to the TES sites), the bed file looks like below:
chr1 148402714 148402875
chr1 149636765 149636929
chr1 202604267 202605293

But the final result peaks' direction is totally different. So I want to know which bed file is right one, why it will cause different result. When I make the metagene plot, does the "chr, start, end" inormation is enough, or do I also need other information in the bed file, such as strand informaiton.

Looking forward to your reply.