Bioconductor Problem With Maketranscriptdbfrombiomart (Genomicfeatures Package)
1
1
Entering edit mode
13.1 years ago
Travis ★ 2.8k

Hi,

I am attempting to retrieve Ensembl transcript annotation using getChromInfoFromBiomart for some RNA-Seq analysis in R.

I am following the manual and using the following command:

makeTranscriptDbFromBiomart(biomart="ensembl",
dataset="hsapiens_gene_ensembl",
transcript_ids=NULL,
circ_seqs=DEFAULT_CIRC_SEQS)

however I get the following screen output and error:

Download and preprocess the 'transcripts' data frame ... Error in
.makeBiomartTranscripts(filters, values, mart, transcript_ids = NULL) :
the 'ensembl_transcript_id' attribute contains duplicated values

Has anyone else experienced a problem like this? Is there a workaround?

Thanks in advance.

SessionInfo() output is included below.

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.4.5 GenomicRanges_1.4.8   IRanges_1.10.6       

loaded via a namespace (and not attached):
[1] biomaRt_2.8.1      Biostrings_2.20.4  BSgenome_1.20.1    DBI_0.2-5         
[5] RCurl_1.6-10       RSQLite_0.10.0     rtracklayer_1.12.5 XML_3.4-3
r rna bioconductor next-gen sequencing • 4.2k views
ADD COMMENT •
0
Entering edit mode

can you give the output of sessionInfo()

ADD REPLY •
0
Entering edit mode

version 2.13.1 (2011-07-08) Platform: x86_64-pc-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] GenomicFeatures_1.4.5 GenomicRanges_1.4.

ADD REPLY •
0
Entering edit mode

version 2.13.1 (2011-07-08) Platform: x86_64-pc-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] GenomicFeatures_1.4.5 GenomicRanges_1.4.

ADD REPLY •
0
Entering edit mode

I have updated the question Jeremy

ADD REPLY •
1
Entering edit mode
13.1 years ago

I think there is something amiss with either Biomart or Ensembl.

library(biomarRt)
.A1_ATTRIBS <- c("ensembl_transcript_id",
             "chromosome_name",
             "strand",
             "transcript_start",
             "transcript_end")
mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
filters <- values <- ""
bm_table <- getBM(.A1_ATTRIBS, filters=filters, values=values, mart=mart)
transcripts_tx_name <- bm_table$ensembl_transcript_id
print(sort(transcripts_tx_name[duplicated(transcripts_tx_name)]))

  [1] "ENST00000244174" "ENST00000262640" "ENST00000285718" "ENST00000286448" "ENST00000302805" "ENST00000313871"
  [7] "ENST00000326153" "ENST00000331035" "ENST00000334060" "ENST00000334651" "ENST00000340131" "ENST00000355432"
 [13] "ENST00000355805" "ENST00000359512" "ENST00000361536" "ENST00000369423" "ENST00000369437" "ENST00000381177"
 [19] "ENST00000381180" "ENST00000381184" "ENST00000381187" "ENST00000381192" "ENST00000381218" "ENST00000381222"
 [25] "ENST00000381223" "ENST00000381229" "ENST00000381233" "ENST00000381241" "ENST00000381261" "ENST00000381297"
 [31] "ENST00000381317" "ENST00000381333" "ENST00000381401" "ENST00000381469" "ENST00000381500" "ENST00000381507"
 [37] "ENST00000381509" "ENST00000381524" "ENST00000381529" "ENST00000381566" "ENST00000381567" "ENST00000381575"
 [43] "ENST00000381578" "ENST00000381625" "ENST00000381657" "ENST00000381663" "ENST00000390665" "ENST00000391707"
 [49] "ENST00000399012" "ENST00000399966" "ENST00000400701" "ENST00000400841" "ENST00000411342" "ENST00000412290"
 [55] "ENST00000412516" "ENST00000412936" "ENST00000414513" "ENST00000415337" "ENST00000416733" "ENST00000417535"
 [61] "ENST00000419094" "ENST00000419737" "ENST00000420411" "ENST00000420865" "ENST00000421233" "ENST00000422618"
 [67] "ENST00000424344" "ENST00000425740" "ENST00000427886" "ENST00000429181" "ENST00000430235" "ENST00000430536"
 [73] "ENST00000430562" "ENST00000430923" "ENST00000431238" "ENST00000431582" "ENST00000431919" "ENST00000432272"
 [79] "ENST00000432318" "ENST00000432523" "ENST00000432757" "ENST00000434938" "ENST00000435581" "ENST00000436474"
 [85] "ENST00000437244" "ENST00000441131" "ENST00000443019" "ENST00000443929" "ENST00000444280" "ENST00000445062"
 [91] "ENST00000445777" "ENST00000445785" "ENST00000445792" "ENST00000447472" "ENST00000447786" "ENST00000448477"
 [97] "ENST00000449611" "ENST00000452144" "ENST00000453953" "ENST00000455739" "ENST00000456370" "ENST00000460206"
[103] "ENST00000460621" "ENST00000460672" "ENST00000461007" "ENST00000461691" "ENST00000462195" "ENST00000463317"
[109] "ENST00000463763" "ENST00000464205" "ENST00000464935" "ENST00000467626" "ENST00000468169" "ENST00000469624"
[115] "ENST00000474361" "ENST00000474865" "ENST00000475167" "ENST00000475259" "ENST00000475594" "ENST00000475859"
[121] "ENST00000476066" "ENST00000477110" "ENST00000477636" "ENST00000477940" "ENST00000478256" "ENST00000478825"
[127] "ENST00000479401" "ENST00000479438" "ENST00000479687" "ENST00000481245" "ENST00000482170" "ENST00000482293"
[133] "ENST00000482405" "ENST00000483079" "ENST00000483286" "ENST00000483543" "ENST00000484026" "ENST00000484364"
[139] "ENST00000484415" "ENST00000484611" "ENST00000485332" "ENST00000486791" "ENST00000488344" "ENST00000489233"
[145] "ENST00000491683" "ENST00000492963" "ENST00000493312" "ENST00000494962" "ENST00000494969" "ENST00000496011"
[151] "ENST00000496301" "ENST00000496630" "ENST00000497752" "ENST00000498153" "ENST00000501036" "ENST00000503018"
[157] "ENST00000507418" "ENST00000509780" "ENST00000515319" "ENST00000527459" "ENST00000534940" "ENST00000540897"
[163] "ENST00000554971"

If I go http://www.biomart.org/biomart/martview/

and search for ENST00000244174

I get two duplicate entries, so a temporary and less than ideal solution is to skip these duplicated transcripts (run the code above the fold first):

"%!in%" <- function(x, y) !(x %in% y)
really_unique<-function(x){x[x %!in% x[duplicated(x)]]}
makeTranscriptDbFromBiomart(biomart="ensembl",
  dataset="hsapiens_gene_ensembl",
  transcript_ids=really_unique(transcripts_tx_name)
)
ADD COMMENT •
0
Entering edit mode

Thanks the help Jeremy.

When I run your code I get this error:

Download and preprocess the 'transcripts' data frame ... V1 1 2 <html><head> 3 <title>500 Internal Server Error</title> 4 </head><body> 5

Internal Server Error

6

The server encountered an internal error or Error in getBM(.A1_ATTRIBS, filters = filters, values = values, mart = mart) : The query to the BioMart webservice ret

ADD REPLY •
0
Entering edit mode

urned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.

ADD REPLY •
0
Entering edit mode

sorry which command generated the error?

ADD REPLY •
0
Entering edit mode

I have raised the issue with Biomart. It might be a bug or a feature. https://lists.biomart.org/pipermail/users/2011-November/001052.html

ADD REPLY •
0
Entering edit mode

Thanks for contacting Biomart Jeremy. I tried to access the bioconductor mailing list also but my message keeps bouncing back. The error appears when I run this command: makeTranscriptDbFromBiomart(biomart="ensembl", + dataset="hsapiens_gene_ensembl", + transcript_ids=really_unique(transcripts_tx_name) + )

ADD REPLY •
0
Entering edit mode

Rhoda Kinsella from EBI has explained the duplicate situation: https://lists.biomart.org/pipermail/users/2011-November/001053.html

not sure what is causing the error in my script

ADD REPLY •
0
Entering edit mode

No problem Jeremy - thanks for all your input

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1758 users visited in the last hour
Content Search
Users
Tags
Badges
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