Closed AAA-3 closed 2 years ago
Can you show the output of:
head(Annotation(brain))
head(Fragments(brain)[[1]])
They are different, like in #826
I guess this has to do with the version of the packages I'm using. I will need to upgrade R and then see if it works.
You need to make sure the line seqlevelsStyle(annotations) <- 'UCSC'
runs successfully without error. In this case the annotations are not UCSC style, so my guess is there was an error somewhere.
Running
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "mm10"
gave an error described here: https://github.com/Bioconductor/GenomeInfoDb/issues/32#issuecomment-965939826_
Running
genome(annotations) <- "mm10"
seqlevelsStyle(annotations) <- 'UCSC'
did not produce an error. The error is resolved by updating to BioC 3.14 which also means upgrading my R which is on 4.0.4. Wanted to avoid having to seek out the administrators but looks like it cant be helped.
Thanks Tim!! :D
Hi @timoast !
I upgraded everything and am still having some issues with the vignette:
I get no errors only warnings which I believe I can ignore (?)
Yet, I am still unable to match annotation styles. Any idea what could be goind wrong?
Embarrassing, but the solution was changing seqlevelsStyle(annotations) <- 'UCSC'
to seqlevelsStyle(annotations) <- "UCSC"
Hi! I updated everything as described in this thread, changed to seqlevelsStyle(annotations) <- 'UCSC', but the error persisted. Would appreciate any suggestions!
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)
Matrix products: default
BLAS/LAPACK: /data/cli_anaconda3/cli_conda_env/newR/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 ggplot2_3.3.5 EnsDb.Hsapiens.v75_2.99.0 ensembldb_2.18.2
[5] AnnotationFilter_1.18.0 GenomicFeatures_1.46.1 AnnotationDbi_1.56.2 Biobase_2.54.0
[9] GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3
[13] BiocGenerics_0.40.0 SeuratObject_4.0.4 Seurat_4.0.6 Signac_1.5.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.22 tidyselect_1.1.1 RSQLite_2.2.9
[5] htmlwidgets_1.5.4 grid_4.1.0 docopt_0.7.1 BiocParallel_1.28.3
[9] Rtsne_0.15 munsell_0.5.0 codetools_0.2-18 ica_1.0-2
[13] future_1.23.0 miniUI_0.1.1.1 withr_2.4.3 colorspace_2.0-2
[17] filelock_1.0.2 knitr_1.37 rstudioapi_0.13 ROCR_1.0-11
[21] tensor_1.5 listenv_0.8.0 MatrixGenerics_1.6.0 slam_0.1-49
[25] GenomeInfoDbData_1.2.7 polyclip_1.10-0 bit64_4.0.5 farver_2.1.0
[29] parallelly_1.30.0 vctrs_0.3.8 generics_0.1.1 xfun_0.29
[33] biovizBase_1.42.0 BiocFileCache_2.2.0 lsa_0.73.2 ggseqlogo_0.1
[37] R6_2.5.1 hdf5r_1.3.5 bitops_1.0-7 spatstat.utils_2.3-0
[41] cachem_1.0.6 DelayedArray_0.20.0 assertthat_0.2.1 promises_1.2.0.1
[45] BiocIO_1.4.0 scales_1.1.1 nnet_7.3-16 gtable_0.3.0
[49] globals_0.14.0 goftest_1.2-3 rlang_0.4.12 RcppRoll_0.3.0
[53] splines_4.1.0 rtracklayer_1.54.0 lazyeval_0.2.2 dichromat_2.0-0
[57] checkmate_2.0.0 spatstat.geom_2.3-1 BiocManager_1.30.16 yaml_2.2.1
[61] reshape2_1.4.4 abind_1.4-5 backports_1.4.1 httpuv_1.6.4
[65] Hmisc_4.6-0 tools_4.1.0 ellipsis_0.3.2 spatstat.core_2.3-2
[69] RColorBrewer_1.1-2 ggridges_0.5.3 Rcpp_1.0.7 plyr_1.8.6
[73] base64enc_0.1-3 progress_1.2.2 zlibbioc_1.40.0 purrr_0.3.4
[77] RCurl_1.98-1.5 prettyunits_1.1.1 rpart_4.1-15 deldir_1.0-6
[81] pbapply_1.5-0 cowplot_1.1.1 zoo_1.8-9 SummarizedExperiment_1.24.0
[85] ggrepel_0.9.1 cluster_2.1.2 magrittr_2.0.1 data.table_1.14.2
[89] scattermore_0.7 lmtest_0.9-39 RANN_2.6.1 SnowballC_0.7.0
[93] ProtGenerics_1.26.0 fitdistrplus_1.1-6 matrixStats_0.61.0 hms_1.1.1
[97] mime_0.12 xtable_1.8-4 XML_3.99-0.8 jpeg_0.1-9
[101] sparsesvd_0.2 gridExtra_2.3 compiler_4.1.0 biomaRt_2.50.1
[105] tibble_3.1.6 KernSmooth_2.23-20 crayon_1.4.2 htmltools_0.5.2
[109] mgcv_1.8-38 later_1.3.0 Formula_1.2-4 tidyr_1.1.4
[113] DBI_1.1.2 tweenr_1.0.2 dbplyr_2.1.1 MASS_7.3-54
[117] rappdirs_0.3.3 Matrix_1.4-0 parallel_4.1.0 igraph_1.2.10
[121] pkgconfig_2.0.3 GenomicAlignments_1.30.0 foreign_0.8-81 plotly_4.10.0
[125] spatstat.sparse_2.1-0 xml2_1.3.3 XVector_0.34.0 VariantAnnotation_1.40.0
[129] stringr_1.4.0 digest_0.6.29 sctransform_0.3.2 RcppAnnoy_0.0.19
[133] spatstat.data_2.1-2 Biostrings_2.62.0 leiden_0.3.9 fastmatch_1.1-3
[137] htmlTable_2.3.0 uwot_0.1.11 restfulr_0.0.13 curl_4.3.2
[141] shiny_1.7.1 Rsamtools_2.10.0 rjson_0.2.20 lifecycle_1.0.1
[145] nlme_3.1-153 jsonlite_1.7.2 BSgenome_1.62.0 viridisLite_0.4.0
[149] fansi_0.5.0 pillar_1.6.4 lattice_0.20-45 KEGGREST_1.34.0
[153] fastmap_1.1.0 httr_1.4.2 survival_3.2-13 glue_1.6.0
[157] qlcMatrix_0.9.7 png_0.1-7 bit_4.0.4 ggforce_0.3.3
[161] stringi_1.7.6 blob_1.2.2 latticeExtra_0.6-29 memoise_2.0.1
[165] dplyr_1.0.7 irlba_2.3.5 future.apply_1.8.1
We used the exact same codes as the pbmc3k vignette: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
Resolved by manually changing the annotations object! Thank you
Resolved by manually changing the annotations object! Thank you
How did you manually change the object? Thanks in advance!
I would like it also, How you manually modify annotations object? Thanks in advance!
I also have those error, I found when as this step they can do well.
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
seqlevels(annotations) <- paste0('chr', seqlevels(annotations)) genome(annotations) <- "hg19" library(ggplot2) library(patchwork)
Annotation(pbmc) <- annotations
but when you not run this" annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)" ,will have this error, even have annotations object. So every time you need run " annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)" for new sample.
Resolved by manually changing the annotations object! Thank you
How?
Hello,
I am teaching myself ATAC analysis and was following the mouse vignette instructions. When I run the code
brain <- TSSEnrichment(brain, fast = FALSE)
, I get the following error:I have looked at #374 #485 #594. Since I am using the vignette data, I do not think it is a gene annoation problem and the
gene_biotype
addition didn't help either (got aGene annotation does not contain gene_biotype information
error instead of the error above).Is this because:
seqlevelsStyle(annotations) <- 'UCSC'
beforegenome(annotations) <- "mm10"
I get an error)GenomeInfoDb
package is not the most recent?Sessioninfo:
Code: