Mapping genes on chromosomes

Question

[1234anjalianjali1234]

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

[GenoMax]

Have you checked on the solution suggested in the error you received?

use the listMarts function to see which BioMart databases are available

[1234anjalianjali1234]

yup..

listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 91
2   ENSEMBL_MART_MOUSE      Mouse strains 91
3     ENSEMBL_MART_SNP  Ensembl Variation 91
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 91

also i tried..

listMarts(host="plants.ensembl.org")
            biomart                      version
1       plants_mart      Ensembl Plants Genes 37
2 plants_variations Ensembl Plants Variations 37

[WouterDeCoster]

hi 1234anjalianjali1234,

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 1

[cpad0112]

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          
>

[1234anjalianjali1234]

Thankyou,

Now can you please solve my original problem of mapping these genes on chromosomes.

>getBM(attributes=c("ensembl_gene_id","chromosome_name","start_position","end_position", "strand"), filters = 'ensembl_gene_id', values = "PGSC0003DMG400029744,PGSC0003DMG400027797,PGSC0003DMG400026469,PGSC0003DMG400013627,PGSC0003DMG400020935,PGSC0003DMG400022602,PGSC0003DMG402022603,PGSC0003DMG400010965,PGSC0003DMG400031318,PGSC0003DMG403026432,PGSC0003DMG404026432,PGSC0003DMG400007743,PGSC0003DMG400020580,PGSC0003DMG401020581", mart = mart)

enter code here
    No encoding supplied: defaulting to UTF-8.
            ensembl_gene_id chromosome_name start_position end_position strand
    1  PGSC0003DMG400007743               9       59441573     59449149     -1
    2  PGSC0003DMG400010965               6       46762379     46763935     -1
    3  PGSC0003DMG400013627               2       37802516     37808556      1
    4  PGSC0003DMG400020580               9       59712402     59712980      1
    5  PGSC0003DMG400020935               4       21192456     21196161      1
    6  PGSC0003DMG400022602               5        6526381      6526863      1
    7  PGSC0003DMG400026469              12       50704471     50704855      1
    8  PGSC0003DMG400027797              11        9730445      9736116      1
    9  PGSC0003DMG400029744               1       81566672     81567534     -1
    10 PGSC0003DMG400031318               6       46918570     46923865     -1
    11 PGSC0003DMG401020581               9       59721273     59722508      1
    12 PGSC0003DMG402022603               5        6537348      6538458      1
    13 PGSC0003DMG403026432               9       59382012     59383726     -1
    14 PGSC0003DMG404026432               9       59385823     59386293     -1

My session info:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8   
 [6] LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] quantsmooth_1.44.0               quantreg_5.34                    SparseM_1.77                     Gviz_1.22.2                     
 [5] devtools_1.13.4                  GenomeGraphs_1.38.0              biomaRt_2.34.1                   BSgenome.Celegans.UCSC.ce6_1.4.0
 [9] BSgenome.Osativa.MSU.MSU7_0.99.1 BiocInstaller_1.28.0             karyoploteR_1.4.1                regioneR_1.10.0                 
[13] BSgenome_1.46.0                  rtracklayer_1.38.2               Biostrings_2.46.0                XVector_0.18.0                  
[17] GenomicRanges_1.30.1             GenomeInfoDb_1.14.0              IRanges_2.12.0                   S4Vectors_0.16.0                
[21] BiocGenerics_0.24.0              memoise_1.1.0

[GenoMax]

Now can you please solve my original problem of mapping these genes on chromosomes.

Isn't that information in the table you posted below that comment?

[1234anjalianjali1234]

I have the information about gene positions but i dont know how to plot these on chromosome.... i mean i want to draw chromosome ideogram...

[GenoMax]

Drawing yeast chromosome ideograms with data
Drawing Chromosome Ideograms With Data
Which Tool Is Used To Plot The Ideogram Shown Here?
Visualize Chromosome With Python ?

[1234anjalianjali1234]

thankyou,

I got my ideogram, but could someone tell me about cytoband information (where to find?).

[GenoMax]

Since cytobands require experimental data, unless someone has done that experiment you would not be able to add that information.

[1234anjalianjali1234]

Thakyou for this reply.

I made my ideogram using Phenogram.