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BiomartGeneRegionTrack for ZNF597 #99

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SmirnygaTotoshka opened this issue Mar 2, 2025 · 0 comments
Open

BiomartGeneRegionTrack for ZNF597 #99

SmirnygaTotoshka opened this issue Mar 2, 2025 · 0 comments

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@SmirnygaTotoshka
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Good afternoon. I have tried to plot ZNF597 scheme using this code.

`
target_region = GRanges("chr16:3431000-3444000")
gtrack <- GenomeAxisTrack(range = target_region,
genome = "hg38",fontsize=12)
bm <- useEnsembl(biomart = "genes",
dataset = "hsapiens_gene_ensembl")
biomTrack <- BiomartGeneRegionTrack(genome = "hg38", chromosome = "chr16",
start = 3431000, end = 3444000,
name = "ZNF597",
filter = list(ensembl_transcript_id="ENST00000301744"),
biomart = bm, utr3 = "blue", utr5 = "green")

plotTracks(list(gtrack,biomTrack), reverseStrand = TRUE)
`

And I have got this.

Image

I dont understand, why both type UTRs stand before protein coding part. I think this picture are contradicted to ensembl annotation. What I did wrong?

Image

My session info
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

time zone: Europe/Moscow
tzcode source: system (glibc)

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

other attached packages:
[1] biomaRt_2.62.1 plyranges_1.26.0 geneAttribution_1.32.0 GenomicFeatures_1.58.0
[5] AnnotationDbi_1.68.0 Biobase_2.66.0 Gviz_1.50.0 GenomicRanges_1.58.0
[9] GenomeInfoDb_1.42.3 IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0
[13] dplyr_1.1.4 vroom_1.6.5

loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 deldir_2.0-4
[4] gridExtra_2.3 httr2_1.1.0 rlang_1.1.5
[7] magrittr_2.0.3 biovizBase_1.54.0 matrixStats_1.5.0
[10] compiler_4.4.2 RSQLite_2.3.9 png_0.1-8
[13] vctrs_0.6.5 ProtGenerics_1.38.0 stringr_1.5.1
[16] pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[19] backports_1.5.0 dbplyr_2.5.0 XVector_0.46.0
[22] Rsamtools_2.22.0 rmarkdown_2.29 tzdb_0.4.0
[25] UCSC.utils_1.2.0 purrr_1.0.4 bit_4.5.0.1
[28] xfun_0.50 zlibbioc_1.52.0 cachem_1.1.0
[31] jsonlite_1.8.9 progress_1.2.3 blob_1.2.4
[34] DelayedArray_0.32.0 BiocParallel_1.40.0 jpeg_0.1-10
[37] parallel_4.4.2 prettyunits_1.2.0 cluster_2.1.8
[40] VariantAnnotation_1.52.0 R6_2.6.1 stringi_1.8.4
[43] RColorBrewer_1.1-3 rtracklayer_1.66.0 rpart_4.1.24
[46] Rcpp_1.0.14 SummarizedExperiment_1.36.0 knitr_1.49
[49] base64enc_0.1-3 Matrix_1.7-2 nnet_7.3-20
[52] tidyselect_1.2.1 dichromat_2.0-0.1 rstudioapi_0.17.1
[55] abind_1.4-8 yaml_2.3.10 codetools_0.2-20
[58] curl_6.2.0 lattice_0.22-6 tibble_3.2.1
[61] withr_3.0.2 KEGGREST_1.46.0 evaluate_1.0.3
[64] foreign_0.8-88 BiocFileCache_2.14.0 xml2_1.3.6
[67] Biostrings_2.74.1 pillar_1.10.1 filelock_1.0.3
[70] MatrixGenerics_1.18.1 checkmate_2.3.2 generics_0.1.3
[73] RCurl_1.98-1.16 ensembldb_2.30.0 hms_1.1.3
[76] ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0
[79] glue_1.8.0 lazyeval_0.2.2 Hmisc_5.2-2
[82] tools_4.4.2 interp_1.1-6 BiocIO_1.16.0
[85] data.table_1.16.4 BSgenome_1.74.0 GenomicAlignments_1.42.0
[88] XML_3.99-0.18 tidyr_1.3.1 latticeExtra_0.6-30
[91] colorspace_2.1-1 GenomeInfoDbData_1.2.13 htmlTable_2.4.3
[94] restfulr_0.0.15 Formula_1.2-5 cli_3.6.4
[97] rappdirs_0.3.3 S4Arrays_1.6.0 AnnotationFilter_1.30.0
[100] gtable_0.3.6 digest_0.6.37 SparseArray_1.6.1
[103] org.Hs.eg.db_3.20.0 rjson_0.2.23 htmlwidgets_1.6.4
[106] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[109] httr_1.4.7 bit64_4.6.0-1

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