Entering edit mode
7.2 years ago
Seigfried
▴
80
I have a bed file like this
ChrIII_A_nidulans_FGSC_A4 0 10 0.83700
ChrIII_A_nidulans_FGSC_A4 10 43 1.11600
ChrIII_A_nidulans_FGSC_A4 43 59 1.39500
ChrIII_A_nidulans_FGSC_A4 59 65 1.67400
ChrIII_A_nidulans_FGSC_A4 65 74 1.95300
As you can see there are no Strand name columns or Strand orientation column. If I try to import this file into R, it calls the score column as the name column
library(GenomicRanges)
library(rtracklayer)
library(IRanges)
file <- import.bed(file.path('C:/Users/ami/Downloads', file.bdg'))
The output for this is below
GRanges object with 4233716 ranges and 1 metadata column:
seqnames ranges strand | name
<Rle> <IRanges> <Rle> | <character>
[1] ChrIII_A_nidulans_FGSC_A4 [ 1, 10] * | 0.83700
[2] ChrIII_A_nidulans_FGSC_A4 [11, 43] * | 1.11600
[3] ChrIII_A_nidulans_FGSC_A4 [44, 59] * | 1.39500
[4] ChrIII_A_nidulans_FGSC_A4 [60, 65] * | 1.67400
[5] ChrIII_A_nidulans_FGSC_A4 [66, 74] * | 1.95300
... ... ... ... . ...
[4233712] mito_A_nidulans_FGSC_A4 [33211, 33214] * | 8.37000
[4233713] mito_A_nidulans_FGSC_A4 [33215, 33216] * | 8.09100
[4233714] mito_A_nidulans_FGSC_A4 [33217, 33218] * | 7.81200
[4233715] mito_A_nidulans_FGSC_A4 [33219, 33220] * | 7.53300
[4233716] mito_A_nidulans_FGSC_A4 [33221, 33227] * | 7.25400
-------
seqinfo: 9 sequences from an unspecified genome; no seqlengths
My overall objective is to create a TSS line plot using this bed file. How can I load a bed file properly in rtracklayer and ignore these columns?