I just have a question about it that I have tried to create a Granges object with the same coordinates as yours, however, why I feel like the sequences were different?
> gr <- GRanges(gr)
> gr
GRanges object with 1 range and 3 metadata columns:
seqnames ranges strand | ENSG pval dPSI
<Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
2 chr20 50941210-50942030 - | ENSG00000000419 0.17493 -0.0109049
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> getSeq(BSgenome.Hsapiens.UCSC.hg38, gr)
DNAStringSet object of length 1:
width seq names
[1] 821 GTAGGTACATGTGTTACAACTTCTTTATTAGTATAACTACTGGAAATGTAT...TATATATATATATATATATATATATATATATATTCACTTTTTTTTTTGTAG 2
> getSeq(BSgenome.Hsapiens.UCSC.hg38, GRanges("chr20:50941210-50942030"))
DNAStringSet object of length 1:
width seq
[1] 821 CTACAAAAAAAAAAGTGAATATATATATATATATATATATATATATATATATATAAATAAAA...CTTGCTATGAATACATTTCCAGTAGTTATACTAATAAAGAAGTTGTAACACATGTACCTAC
I just feel a bit confused because I use the same coordinates and BSgenome.
Hi!
Thank you so much for providing this.
I just have a question about it that I have tried to create a Granges object with the same coordinates as yours, however, why I feel like the sequences were different?
I just feel a bit confused because I use the same coordinates and BSgenome.
Thank you so much
Your gr is stranded, the sequence is the reverse complement of James version due to strand-aware extraction. Unstranded defaults to positive strand.