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

<Rle> <IRanges> <Rle> | <character> <numeric>

[1] chr1 815093-817883 * | MACS_peak_1 295.76

[2] chr1 1243288-1244338 * | MACS_peak_2 63.19

[3] chr1 2979977-2981228 * | MACS_peak_3 100.16

[4] chr1 3566182-3567876 * | MACS_peak_4 558.89

[5] chr1 3816546-3818111 * | MACS_peak_5 57.57

... ... ... ... . ... ...

[1327] chrX 135244783-135245821 * | MACS_peak_1327 55.54

[1328] chrX 139171964-139173506 * | MACS_peak_1328 270.19

[1329] chrX 139583954-139586126 * | MACS_peak_1329 918.73

[1330] chrX 139592002-139593238 * | MACS_peak_1330 210.88

[1331] chrY 13845134-13845777 * | MACS_peak_1331 58.39

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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.

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