Mapping genes on chromosomes
1
Hellow,
I want to map plant genes on the chromosomes. I have gff file. I tried using biomart but it's giving an error.
library( GenomeGraphs)
library( biomaRt)
library( regioneR)
mart < - useMart( "plants_mart" , host = "plants.ensembl.org" )
listDatasets( mart, verbose = FALSE)
mart < - useMart( "plants_mart" , dataset= "stuberosum_eg_gene" , host = "plants.ensembl.org" )
useEnsembl( biomart = "mart" , dataset = "stuberosum_eg_gene " , host = "plants.ensembl.org" , version = NULL, GRCh = NULL, mirror = NULL, verbose = FALSE)
Error in useMart( biomart = biomart, dataset = dataset, host = host, verbose = verbose,
:
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
mapping
chromosomes
genes
• 2.5k views
library( biomaRt)
mart= useMart( "plants_mart" , host= "plants.ensembl.org" ,"stuberosum_eg_gene" )
getBM( attributes= c( "ensembl_gene_id" ,"chromosome_name" ,"start_position" ,"end_position" , "strand" ) ,
filters = 'ensembl_gene_id' ,
values = "PGSC0003DMG400029744" ,
mart = mart)
output:
No encoding supplied: defaulting to UTF-8.
ensembl_gene_id chromosome_name start_position end_position strand
1 PGSC0003DMG400029744 1 81566672 81567534 -1
btw, gtf file is supposed to have chromosome , coordinates and strand information for a feature.
> sessionInfo( )
R version 3.4.3 ( 2017-11-30)
Platform: x86_64-pc-linux-gnu ( 64-bit)
Running under: Ubuntu 17.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[ 1] LC_CTYPE= en_IN.UTF-8 LC_NUMERIC= C
[ 3] LC_TIME= en_IN.UTF-8 LC_COLLATE= en_IN.UTF-8
[ 5] LC_MONETARY= en_IN.UTF-8 LC_MESSAGES= en_IN.UTF-8
[ 7] LC_PAPER= en_IN.UTF-8 LC_NAME= C
[ 9] LC_ADDRESS= C LC_TELEPHONE= C
[ 11] LC_MEASUREMENT= en_IN.UTF-8 LC_IDENTIFICATION= C
attached base packages:
[ 1] stats graphics grDevices utils datasets methods base
other attached packages:
[ 1] biomaRt_2.34.1
loaded via a namespace ( and not attached) :
[ 1] Rcpp_0.12.14 AnnotationDbi_1.40.0 magrittr_1.5
[ 4] BiocGenerics_0.24.0 progress_1.1.2 IRanges_2.12.0
[ 7] bit_1.1-13 R6_2.2.2 rlang_0.1.6
[ 10] httr_1.3.1 stringr_1.2.0 blob_1.1.0
[ 13] tools_3.4.3 parallel_3.4.3 Biobase_2.38.0
[ 16] DBI_0.7 yaml_2.1.16 bit64_0.9-7
[ 19] digest_0.6.13 assertthat_0.2.0 tibble_1.4.1
[ 22] S4Vectors_0.16.0 bitops_1.0-6 curl_3.1
[ 25] rsconnect_0.8.5 RCurl_1.96-0 memoise_1.1.0
[ 28] RSQLite_2.0 stringi_1.1.6 compiler_3.4.3
[ 31] pillar_1.0.1 prettyunits_1.0.2 stats4_3.4.3
[ 34] XML_3.99-0
>
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Have you checked on the solution suggested in the error you received?
yup..
also i tried..
hi 1234anjalianjali1234,
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