what does " * " denote under the strand column of the GRanges object file output
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Meghna • 0
@c61bc565
Last seen 3 months ago
United States

Hi I am new to analysis. I am trying to do some ATAC analysis. so I was reading through and wanted to understand the file output here is snap shot of the tutorial from http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html seqnames ranges strand | V4 V5

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could you tell me why is there a * under the strand column instead of + / -

ChIPseeker • 159 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

With ATAC-Seq you are detecting regions of accessible DNA, which isn't strand specific, so you shouldn't expect a peak to be on a particular strand.

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Just to add to James' answer. If you look up the help page for strand (using help("strand", "BiocGenerics")) you'll find some documentation, including:

‘*’ is used when the exact strand of the location is unknown, or irrelevant, or when the "feature" at that location belongs to both strands.

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Thanks a lot. I guessed it to be so but just wanted to be sure thanks a lot.