Question: Mapping genes on chromosomes
1
gravatar for 1234anjalianjali1234
18 days ago by
India
1234anjalianjali123420 wrote:

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

chromosomes mapping genes • 163 views
ADD COMMENTlink modified 18 days ago by cpad01124.1k • written 18 days ago by 1234anjalianjali123420

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

use the listMarts function to see which BioMart databases are available

ADD REPLYlink written 18 days ago by genomax40k

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
ADD REPLYlink modified 18 days ago • written 18 days ago by 1234anjalianjali123420

hi 1234anjalianjali1234,

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

ADD REPLYlink written 13 days ago by WouterDeCoster25k
2
gravatar for cpad0112
18 days ago by
cpad01124.1k
cpad01124.1k wrote:
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          
>
ADD COMMENTlink modified 18 days ago • written 18 days ago by cpad01124.1k

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
ADD REPLYlink modified 17 days ago • written 17 days ago by 1234anjalianjali123420

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?

ADD REPLYlink written 17 days ago by genomax40k

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...

ADD REPLYlink modified 16 days ago • written 16 days ago by 1234anjalianjali123420
2

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 ?

ADD REPLYlink modified 16 days ago • written 16 days ago by genomax40k

thankyou,

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

ADD REPLYlink modified 13 days ago • written 13 days ago by 1234anjalianjali123420

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

ADD REPLYlink modified 13 days ago • written 13 days ago by genomax40k

Thakyou for this reply.

I made my ideogram using Phenogram.

ADD REPLYlink written 13 days ago by 1234anjalianjali123420
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