View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
3
0
Entering edit mode
vinod.acear ▴ 50
@vinodacear-8884
Last seen 4.2 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 • 1.3k views
ADD COMMENT
0
Entering edit mode
vinod.acear ▴ 50
@vinodacear-8884
Last seen 4.2 years ago
India

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

ADD COMMENT
0
Entering edit mode
vinod.acear ▴ 50
@vinodacear-8884
Last seen 4.2 years ago
India

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

ADD COMMENT
0
Entering edit mode
@herve-pages-1542
Last seen 16 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.

ADD COMMENT

Login before adding your answer.

Traffic: 937 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6