- Merge the rRNA (and Mt_RNA) genes from the main annotation with the predicted tRNA genes
## R version 3.6.1 (2019-07-05)
## Platform x86_64-pc-linux-gnu (64-bit)
## Running under Ubuntu 18.04.3 LTS
## Last knitted on Fri Aug 23 11:43:55 2019
## Species: Homo sapiens
## Genome assembly: hg19
## Gencode version: 19
If any of the information above does not suit your needs, please review it in the ‘setup’ chunk and re-run the script.
If they are not present in the working folder, the pipeline will download the following files:
- Comprehensive gene annotation: It contains the comprehensive gene annotation on the reference chromosomes only.
- Long non-coding RNA gene annotation: It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes (this is a subset of the main annotation file);
- Predicted tRNA genes: tRNA genes predicted by ENSEMBL on the reference chromosomes using tRNAscan-SE (this dataset does not form part of the main annotation file);
- Chromosome sizes: The file contains the size in nucleorides of each chromosome.
Note: the pipeline will search for the genome assembly and Gencode annotation versions specified within the script. Therefore, if you plan to use a different species/assembly/annotation make sure you change the script accordingly.
| Biotype | 1 | 2 | 3 |
|---|---|---|---|
| protein_coding | 5165 | 14614 | 548 |
| pseudogene | 8823 | 4791 | 306 |
| lincRNA | 1010 | 6097 | 2 |
| antisense | 852 | 4421 | 0 |
| miRNA | 0 | 6 | 3043 |
| misc_RNA | 0 | 2 | 2031 |
| snRNA | 0 | 5 | 1911 |
| snoRNA | 0 | 8 | 1449 |
| sense_intronic | 64 | 677 | 0 |
| rRNA | 0 | 0 | 526 |
The Comprehensive gene annotation file is employed to extract information on genes, transcripts and exons, while the Long non-coding RNA gene annotation is used to include additional non-coding RNAs (assigned as such by Gencode) to those predicted using sequences from Rfam and miRBase.
By default, the analysis is restricted to standard chromosome only, and to level 1 (validated), 2 (manual annotation) and 3 (automated annotation) genes.
-
<genome>_Gencode<version>_genes_annotations_minimal.RData: It contains the basic annotation objects, including genes GRanges and metadata information.
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<genome>_Gencode<version>_txs_annotations_minimal.RData: It contains the basic annotation objects, including transcripts GRanges and metadata information.
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<genome>_Gencode<version>_genes_annotations.RData: In addition to the minimal object, it contains exons GRanges and separate protein-coding and non-coding genes and exons GRanges.
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<genome>_Gencode<version>_txs_annotations.RData: In addition to the minimal object, it contains exons GRanges and separate protein-coding and non-coding longest transcripts and exons GRanges. These are further divided into ‘pre’ (nascent) and ‘rna’ (mature) transcripts.
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<genome>_Gencode<version>_annotations.pc.transcript.regions.rds: It contains protein-coding genes GRanges sub-divided into 5’-UTR, exonic and 3’-UTR regions.
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<genome>_Gencode<version>_annotations.all.genes.transcript.regions.rds: It contains all the annotated features, where each annotated nucleotide is assigned to a transcript biotype using the following hierarchy: ncRNA > cds > utr3 > utr5 > intron > other > intergenic
| Region | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. | Coverage |
|---|---|---|---|---|---|---|---|
| UTR5 | 1 | 95 | 204 | 300.7 | 375 | 14960 | 5746629 |
| CDS | 8 | 687 | 1191 | 1619.2 | 1965 | 107976 | 33280413 |
| UTR3 | 1 | 355 | 933 | 1517.0 | 2061 | 22552 | 29321630 |
| Group | Region | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. | Coverage |
|---|---|---|---|---|---|---|---|---|
| ncRNA | exon | 1 | 87.0 | 104.0 | 125.2 | 121.0 | 1559 | 1110549 |
| long_ncRNA | exon | 1 | 103.0 | 178.0 | 383.0 | 362.0 | 91667 | 17231198 |
| long_ncRNA | intron | 1 | 647.0 | 2147.0 | 9225.7 | 7837.0 | 409122 | 320169286 |
| protein_coding | CDS | 1 | 82.0 | 121.0 | 168.6 | 171.0 | 21693 | 35239515 |
| protein_coding | five_prime_UTR | 1 | 67.0 | 128.0 | 198.8 | 240.0 | 14960 | 9098634 |
| protein_coding | three_prime_UTR | 1 | 113.0 | 367.0 | 935.6 | 1169.0 | 22552 | 33261185 |
| protein_coding | intron | 1 | 475.2 | 1494.0 | 5387.0 | 4203.0 | 657297 | 1179276593 |
| protein_coding | exon | 1 | 86.0 | 176.0 | 321.4 | 350.0 | 24177 | 16342578 |
| protein_coding | UTR | 4 | 71.2 | 111.5 | 353.7 | 161.8 | 15046 | 72864 |
| other | exon | 1 | 120.0 | 238.0 | 426.0 | 541.0 | 12496 | 11727581 |
| other | intron | 1 | 309.0 | 829.0 | 2666.0 | 2273.0 | 311063 | 34537801 |
| other | CDS | 4 | 96.0 | 136.0 | 191.8 | 181.0 | 1859 | 73467 |
| other | three_prime_UTR | 10 | 121.5 | 314.0 | 604.8 | 762.0 | 3328 | 18750 |
| other | five_prime_UTR | 2 | 35.0 | 89.0 | 98.0 | 123.0 | 352 | 3235 |
| Region | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. | Coverage |
|---|---|---|---|---|---|---|---|
| ncRNA | 35 | 87 | 104 | 125.4 | 121.0 | 2728 | 1147867 |
| CDS | 1 | 84 | 123 | 170.7 | 172.0 | 21693 | 35101038 |
| UTR3 | 1 | 188 | 541 | 1116.8 | 1460.5 | 22552 | 31846862 |
| UTR5 | 1 | 67 | 126 | 196.9 | 238.0 | 14960 | 8998336 |
| long_ncRNA | 1 | 91 | 160 | 325.2 | 317.0 | 91667 | 24356623 |
| intron | 1 | 449 | 1425 | 5247.9 | 3995.0 | 728468 | 1162213235 |
| other | 1 | 472 | 1350 | 7480.1 | 5488.5 | 602638 | 393624369 |