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Genes called present in an RNA-Seq library are often defined using an abitrary cutoff of log2(TPM) = 1. BgeeCall allows to calculate a library specific cutoff. Reference intergenic sequences are the key element to define this library secific TPM cutoff. The cutoff is defined with the equation :
\[ \frac {proportion\ of\ reference\ intergenic\ present}{proportion\ of\ protein\ coding\ present} = 0.05 \]
This section describes the different releases of reference intergenic that are available and explain how to get information of species available in each release. In this practical we will only use the last official Bgee intergenic release.
To list all available intergenic releases run the function :
releases <- list_intergenic_release()Downloading release information of reference intergenic sequences...subset(releases, select=c(release, releaseDate, description)) release releaseDate
1 0.1 2018-12-21
2 0.2 2019-02-07
3 community 2019-07-22
4 custom 2019-07-22
description
1 intergenic regions used to generate Bgee 14.
2 cleaned intergenic sequences based on release 0.1 (remove blocks of Ns longer than 100 and sequences containing more than 5% of Ns).
3 Release allowing to access to all reference intergenic sequences generated by the community and not present in Bgee for the moment.
4 Release allowing to use your own FASTA reference intergenic sequences. When this release is selected BgeeCall will use the sequences at UserMetadata@custom_intergenic_path to generate present/absent calls.In this list the first line always correspond to last official Bgee release.
All releases for which the name is a number are Bgee releases. It means all reference intergenic sequences from these releases have been generated by the Bgee team. It is possible to list all species available in one bgee release with the commands :
# create an object of the class BgeeMetadata using Bgee release 0.2
bgee <- new("BgeeMetadata")
Querying Bgee to get intergenic release information...# list species available for this release
list_bgee_ref_intergenic_species(bgee) speciesId speciesName numberOfLibraries genomeVersion
1 9606 Homo sapiens 5026 GRCh38.p5
2 10090 Mus musculus 133 GRCm38.p4
3 9544 Macaca mulatta 90 MMUL1.0
4 7955 Danio rerio 67 GRCz10
5 8364 Xenopus tropicalis 66 JGI4.2
6 6239 Caenorhabditis elegans 50 WBcel235
7 9031 Gallus gallus 45 Galgal4
8 10116 Rattus norvegicus 36 Rnor_6.0
9 9913 Bos taurus 33 UMD3.1
10 13616 Monodelphis domestica 19 monDom5
11 9258 Ornithorhynchus anatinus 17 OANA5
12 7240 Drosophila simulans 17 GCA_000259055.1
13 9598 Pan troglodytes 15 CHIMP2.1.4
14 7237 Drosophila pseudoobscura 14 GCA_000001765.2
15 7227 Drosophila melanogaster 14 BDGP6
16 9593 Gorilla gorilla 13 gorGor3.1
17 9597 Pan paniscus 12 CHIMP2.1.4
18 9823 Sus scrofa 10 Sscrofa10.2
19 10141 Cavia porcellus 9 Felis_catus_6.2
20 9685 Felis catus 9 cavPor3
21 7230 Drosophila mojavensis 8 EquCab2
22 9796 Equus caballus 8 GCA_000005175.1
23 9986 Oryctolagus cuniculus 6 eriEur1
24 9615 Canis lupus familiaris 6 CanFam3.1
25 9365 Erinaceus europaeus 6 OryCun2.0
26 7244 Drosophila virilis 4 GCA_000005245.1
27 28377 Anolis carolinensis 4 AnoCar2.0
28 7217 Drosophila ananassae 4 GCA_000005975.1
29 7245 Drosophila yakuba 4 GCA_000005115.1If your species of interest is not present in the last official intergenic release you can check if the BgeeCall community already generated the reference intergenic sequences. To do so use the commands :
list_community_ref_intergenic_species() speciesId numberOfLibraries annotationVersion genomeVersion kallistoVersion
1 10036 15 MesAur1.0 MesAur1.0 0.46.0
2 13686 243 Si_gnG Si_gnG 0.44.0
url
1 https://zenodo.org/api/files/f46c7de0-d9a5-4ffd-a30e-4b08121ba446/ref_intergenic.fa.gz
2 https://zenodo.org/api/files/5492ff2f-91a3-4101-8d67-78b8f8625cc6/ref_intergenic.fa.gzIt is possible to use these species in BgeeCall with the commands :
bgee <- new("BgeeMetadata", intergenic_release="community")
Querying Bgee to get intergenic release information...IMPORTANT : These reference intergenic sequences have not been generated by Bgee. Use with caution.If you did not find your species, you can participate to the community and generate your own reference intergenic sequences. A tutorial describing prerequisites and all steps is available here
This release allows not to download reference intergenic sequences but import them from a file.
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
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_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BgeeCall_1.2.1 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 lattice_0.20-41
[3] prettyunits_1.1.1 Rsamtools_2.2.3
[5] Biostrings_2.54.0 assertthat_0.2.1
[7] rprojroot_1.3-2 digest_0.6.25
[9] BiocFileCache_1.10.2 R6_2.4.1
[11] GenomeInfoDb_1.22.0 backports_1.1.5
[13] stats4_3.6.3 RSQLite_2.2.0
[15] evaluate_0.14 httr_1.4.1
[17] pillar_1.4.3 zlibbioc_1.32.0
[19] rlang_0.4.5 GenomicFeatures_1.38.2
[21] progress_1.2.2 curl_4.3
[23] whisker_0.4 blob_1.2.1
[25] S4Vectors_0.24.3 Matrix_1.2-18
[27] rmarkdown_2.1 BiocParallel_1.20.1
[29] stringr_1.4.0 RCurl_1.98-1.1
[31] bit_1.1-15.2 biomaRt_2.42.0
[33] DelayedArray_0.12.2 compiler_3.6.3
[35] httpuv_1.5.2 rtracklayer_1.46.0
[37] xfun_0.12 pkgconfig_2.0.3
[39] askpass_1.1 BiocGenerics_0.32.0
[41] htmltools_0.4.0 tximport_1.14.0
[43] openssl_1.4.1 tidyselect_1.0.0
[45] SummarizedExperiment_1.16.1 tibble_2.1.3
[47] GenomeInfoDbData_1.2.2 matrixStats_0.55.0
[49] IRanges_2.20.2 XML_3.99-0.3
[51] crayon_1.3.4 dplyr_0.8.4
[53] dbplyr_1.4.2 later_1.0.0
[55] GenomicAlignments_1.22.1 bitops_1.0-6
[57] rappdirs_0.3.1 grid_3.6.3
[59] jsonlite_1.6.1 DBI_1.1.0
[61] git2r_0.26.1 magrittr_1.5
[63] stringi_1.4.6 XVector_0.26.0
[65] fs_1.3.2 promises_1.1.0
[67] vctrs_0.2.3 Rhdf5lib_1.8.0
[69] tools_3.6.3 bit64_0.9-7
[71] Biobase_2.46.0 glue_1.3.1
[73] purrr_0.3.3 hms_0.5.3
[75] parallel_3.6.3 yaml_2.2.1
[77] rhdf5_2.30.1 AnnotationDbi_1.48.0
[79] GenomicRanges_1.38.0 memoise_1.1.0
[81] knitr_1.28