View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 2.3 years ago
India

hi please help in getting sub-sequences in View, corresponding to granges on positive strand and reverse complementary of granges on negative strand. 

Views granges grangeslist iranges • 801 views
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 2.3 years ago
India

Got answer for that Views by default give +ve strand sequence for both granges of both strand. 

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vinod.acear ▴ 50
@vinodacear-8884
Last seen 2.3 years ago
India

Got answer for that Views by default give +ve strand sequence for both granges of both strand. 

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@herve-pages-1542
Last seen 20 hours ago
Seattle, WA, United States

Hi,

If you want to create views on a BSgenome object (e.g. views on the exons of the Human genome) then:

library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
ex <- exons(txdb)
v <- Views(genome, ex)
v
# BSgenomeViews object with 289969 views and 1 metadata column:
#                seqnames         ranges strand             dna  |
#                   <Rle>      <IRanges>  <Rle>  <DNAStringSet>  |
#      [1]           chr1 [11874, 12227]      + [CTTGC...GGCCA]  |
#      [2]           chr1 [12595, 12721]      + [GCTCC...CAGAG]  |
#      [3]           chr1 [12613, 12721]      + [GTGTG...CAGAG]  |
#      [4]           chr1 [12646, 12697]      + [CATCA...CTCTT]  |
#      [5]           chr1 [13221, 14409]      + [GCAGG...TTCTG]  |
#      ...            ...            ...    ...             ... ..
# [289965] chrUn_gl000241 [35706, 35859]      - [GCGAG...AAGTG]  |
# [289966] chrUn_gl000241 [36711, 36875]      - [CTCCA...AAGAG]  |
# [289967] chrUn_gl000243 [11501, 11530]      + [TGGTG...AAGAA]  |
# [289968] chrUn_gl000243 [13608, 13637]      + [TTGCA...GAGCC]  |
# [289969] chrUn_gl000247 [ 5787,  5816]      - [TGGTG...AAGAA]  |
#            exon_id
#          <integer>
#      [1]         1
#      [2]         2
#      [3]         3
#      [4]         4
#      [5]         5
#      ...       ...
# [289965]    289965
# [289966]    289966
# [289967]    289967
# [289968]    289968
# [289969]    289969
# -------
# seqinfo: 93 sequences (1 circular) from hg19 genome

See ?BSgenomeViews in the BSgenome package for more information.

H.

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