Gviz: Possible 5' and 3' marker errors
0
0
Entering edit mode
stianlagstad ▴ 90
@stianlagstad-9723
Last seen 4.8 years ago

This code:
```
transcriptID <- "ENST00000395443"

mart <- biomaRt::useMart(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl",
  host = "dec2013.archive.ensembl.org")

# Create transcript track
biomartTrack <- Gviz::BiomartGeneRegionTrack(
  filters = list(
    ensembl_transcript_id = transcriptID),
  biomart = mart)

# Create axis track
axisTrack <- Gviz::GenomeAxisTrack()
displayPars(axisTrack) <- list(
  add53 = TRUE,
  labelPos = "below",
  cex = 1.5
)

Gviz::plotTracks(
  c(biomartTrack, axisTrack),
  chromosome = "chr3",
  add53 = TRUE,
  add35 = TRUE)
```

Produces this:
Both strands are tagged with 5' on the left and 3' on the right, which is wrong. Is this a bug?

Thank you.

 

software error • 698 views
ADD COMMENT

Login before adding your answer.

Traffic: 596 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