Question: Is there any way to determine whether my sequenced data uses 0- or 1-based coordinates?
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gravatar for biohack92
3.3 years ago by
biohack92150
United States
biohack92150 wrote:

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 modified 3.3 years ago by Alex Reynolds28k • written 3.3 years ago by biohack92150
1
gravatar for Alex Reynolds
3.3 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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 modified 3.3 years ago • written 3.3 years ago by Alex Reynolds28k

Thanks for the explanation.

ADD REPLYlink written 3.3 years ago by biohack92150
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