I'm trying to generate enrichments from different bigwig files for TSS (-100,+500) and gene body (+500, end) for certain TFs using TSS and body coordinates from the same genes ordered in a bed file (the TSS and body bed files rows match). But after I run multibigwigsummary in the -BED mode for TSS and body bed files separately, the resulting txt file is sorted by chromosome or something and the rows don't match anymore. The issue is I am unable to merge using Excel or pandas or R because that would require matching the chromosome in the first column AND start or end coordinates depending on the strand. In my input BED file, the fourth column containing gene names has 'Symbol' as the header and I tried using the option --transcript_id_designator 'Symbol' to preserve the gene name in order to merge later but the resulting output text file did not have gene names. Is there a way to run multibigwig summary where the resulting output text file is not sorted and the regions are matching the original input bed file?
I'm trying to generate enrichments from different bigwig files for TSS (-100,+500) and gene body (+500, end) for certain TFs using TSS and body coordinates from the same genes ordered in a bed file (the TSS and body bed files rows match). But after I run multibigwigsummary in the -BED mode for TSS and body bed files separately, the resulting txt file is sorted by chromosome or something and the rows don't match anymore. The issue is I am unable to merge using Excel or pandas or R because that would require matching the chromosome in the first column AND start or end coordinates depending on the strand. In my input BED file, the fourth column containing gene names has 'Symbol' as the header and I tried using the option --transcript_id_designator 'Symbol' to preserve the gene name in order to merge later but the resulting output text file did not have gene names. Is there a way to run multibigwig summary where the resulting output text file is not sorted and the regions are matching the original input bed file?