Question

browserSession for Arabidopsis

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mfahim • 0

@mfahim-7714

Last seen 9.3 years ago

Korea, Republic Of

Hi everyone,

I am trying to use run splieR for splicing analysis in my RNAseq data from Arabidopsis.

As usual, the packages and instructions in manuals are for anything but plants.

Here is my question

Arabidopsis genome is not listed in UCSC. What should be alternative to the following chunk in spliceR documentation. Cheers.

session <- browserSession("UCSC")
genome(session) <- "hg19"
query <- ucscTableQuery(session, "knownGene")
tableName(query) <- "knownGene"
cdsTable <- getTable(query)

rtracklayer Granges spliceR • 1.8k views

ADD COMMENT • link updated 9.3 years ago by Michael Lawrence ★ 11k • written 9.3 years ago by mfahim • 0

score 0 · Answer 1 · 2015-07-22

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

United States

Sorry, but there is no UCSC genome build for Arapidopsis. Unfortunately, it looks like there is no easy way with spliceR to use TxDb packages. But it just takes some manual work, using the transcripts() and exons() accessors, requesting columns=c("tx_id", "gene_id") and doing all the munging. The relevant TxDb package is "TxDb.Athaliana.BioMart.plantsmart25". You might also check out the "sgseq" package.

ADD COMMENT • link 9.3 years ago Michael Lawrence ★ 11k

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thanks.. is that TAIR10?

and how should I do that?

ADD REPLY • link 9.3 years ago mfahim • 0

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> session <- browserSession("UCSC")
> genome(session) <- "araTha1"
Error in `genome<-`(`*tmp*`, value = "araTha1") : 
  Failed to set session genome to 'araTha1'

and the Error

ADD REPLY • link 9.3 years ago mfahim • 0

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Yea, sorry, I got that identifier from some sort of example of a custom hub. Arabidopsis is not in the actual UCSC database. I'll edit the answer.

ADD REPLY • link 9.3 years ago Michael Lawrence ★ 11k

Arabidopsis genome is not listed in UCSC. What should be alternative to the following chunk in spliceR documentation. Cheers. session <- browserSession("UCSC") genome(session) <- "hg19" query <- ucscTableQuery(session, "knownGene") tableName(query) <- "knownGene" cdsTable <- getTable(query)

Arabidopsis genome is not listed in UCSC. What should be alternative to the following chunk in spliceR documentation. Cheers.

session <- browserSession("UCSC")
genome(session) <- "hg19"
query <- ucscTableQuery(session, "knownGene")
tableName(query) <- "knownGene"
cdsTable <- getTable(query)