Question: Is there any way to determine whether my sequenced data uses 0- or 1-based coordinates?
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I have bisulfite sequencing data that was aligned and provided in bigwig format. I've since converted the files to bedgraph format, and based off the naming of the files, the BS-seq data was split by +/- strand (i.e., sample1 has two bedgraph files, one bedgraph for the reads on the plus strand, and another bedgraph for reads on the negative strand). I noticed that the start and end coordinates on the plus strand sample to be 1 position lower than the negative strand samples. I appreciate any insight in explaining this discrepancy.

ADD COMMENTlink 3.8 years ago biohack92 • 150 • updated 3.8 years ago Alex Reynolds 28k
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If the methylation call or mark or event is generated on the 5' side of the cytosine nucleotide on the 5'-CG-3' on the forward/sense strand, the position of the mark or event on the reverse/antisense strand — to make it on the 5' side of the cytosine on the 3'-GC-5' on the reverse stand — would probably need to be one base "forward" as measured with respect to the methylation event on the forward/sense strand.

ADD COMMENTlink 3.8 years ago Alex Reynolds 28k
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Thanks for the explanation.

ADD REPLYlink 3.8 years ago
biohack92
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