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docs: add marmoset genome to table, update changelog
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kelly-sovacool committed Dec 3, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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- Fix spelling of shared SIF directory on biowulf -- it is `/data/CCBR_Pipeliner/SIFs` with a lowercase "s" at the end. (#182, @kelly-sovacool)
- Raise an error if too few reads are left after trimming with cutadapt. (#184, @kelly-sovacool)
- Reformat GTF files during `renee build` that are missing 'gene_biotype' or 'gene_type' attributes in exons. (#185, @kelly-sovacool)
- Add support for the marmoset genome (mCalJac1 2021). (#185, @kelly-sovacool)

## RENEE 2.6.3

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27 changes: 14 additions & 13 deletions docs/RNA-seq/Resources.md
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Expand Up @@ -9,19 +9,20 @@ The hg38 fasta files were downloaded from the GDC with virus and decoy sequences
while these sequences were manually added to the hg19 fasta from Encode.
See details here: <https://github.com/CCBR/build-renee-refs>

| **Genome** | **Species** | **Annotation Version** | **Notes** |
| ---------- | -------------------- | -------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------- |
| hg19_19 | Homo sapiens (human) | [Gencode Release 19](https://www.gencodegenes.org/human/release_19.html) | [GRCh37](https://www.gencodegenes.org/human/release_19.html), Annotation Release date: 07/2013 |
| hg19_36 | Homo sapiens (human) | [Gencode Release 36-lift-37](https://www.gencodegenes.org/human/release_36lift37.html) | [GRCh37](https://www.gencodegenes.org/human/release_36lift37.html) |
| hg38_30 | Homo sapiens (human) | [Gencode Release 30](https://www.gencodegenes.org/human/release_30.html) | [GRCh38](https://www.gencodegenes.org/human/release_30.html), Annotation Release date: 11/2018 |
| hg38_34 | Homo sapiens (human) | [Gencode Release 34](https://www.gencodegenes.org/human/release_34.html) | [GRCh38](https://www.gencodegenes.org/human/release_34.html), Annotation Release date: 04/2020 |
| hg38_36 | Homo sapiens (human) | [Gencode Release 36](https://www.gencodegenes.org/human/release_36.html) | [GRCh38](https://www.gencodegenes.org/human/release_36.html), Annotation Release date: 05/2020 |
| hg38_38 | Homo sapiens (human) | [Gencode Release 38](https://www.gencodegenes.org/human/release_38.html) | [GRCh38](https://www.gencodegenes.org/human/release_38.html), Annotation Release date: 05/2021 |
| hg38_41 | Homo sapiens (human) | [Gencode Release 41](https://www.gencodegenes.org/human/release_41.html) | [GRCh38](https://www.gencodegenes.org/human/release_41.html), Annotation Release date: 07/2022 |
| hg38_45 | Homo sapiens (human) | [Gencode Release 45](https://www.gencodegenes.org/human/release_45.html) | [GRCh38](https://www.gencodegenes.org/human/release_45.html), Annotation Release date: 03/2023 |
| mm10_M21 | Mus musculus (mouse) | [Gencode Release M21](https://www.gencodegenes.org/mouse/release_M21.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M21.html), Annotation Release date: 04/2019 |
| mm10_M23 | Mus musculus (mouse) | [Gencode Release M23](https://www.gencodegenes.org/mouse/release_M23.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M23.html), Annotation Release date: 09/2019 |
| mm10_M25 | Mus musculus (mouse) | [Gencode Release M25](https://www.gencodegenes.org/mouse/release_M25.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M25.html), Annotation Release date: 04/2020 |
| **Genome** | **Species** | **Annotation Version** | **Notes** |
| ------------- | ---------------------------------------------- | ------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------- |
| hg19_19 | Homo sapiens (human) | [Gencode Release 19](https://www.gencodegenes.org/human/release_19.html) | [GRCh37](https://www.gencodegenes.org/human/release_19.html), Annotation Release date: 07/2013 |
| hg19_36 | Homo sapiens (human) | [Gencode Release 36-lift-37](https://www.gencodegenes.org/human/release_36lift37.html) | [GRCh37](https://www.gencodegenes.org/human/release_36lift37.html) |
| hg38_30 | Homo sapiens (human) | [Gencode Release 30](https://www.gencodegenes.org/human/release_30.html) | [GRCh38](https://www.gencodegenes.org/human/release_30.html), Annotation Release date: 11/2018 |
| hg38_34 | Homo sapiens (human) | [Gencode Release 34](https://www.gencodegenes.org/human/release_34.html) | [GRCh38](https://www.gencodegenes.org/human/release_34.html), Annotation Release date: 04/2020 |
| hg38_36 | Homo sapiens (human) | [Gencode Release 36](https://www.gencodegenes.org/human/release_36.html) | [GRCh38](https://www.gencodegenes.org/human/release_36.html), Annotation Release date: 05/2020 |
| hg38_38 | Homo sapiens (human) | [Gencode Release 38](https://www.gencodegenes.org/human/release_38.html) | [GRCh38](https://www.gencodegenes.org/human/release_38.html), Annotation Release date: 05/2021 |
| hg38_41 | Homo sapiens (human) | [Gencode Release 41](https://www.gencodegenes.org/human/release_41.html) | [GRCh38](https://www.gencodegenes.org/human/release_41.html), Annotation Release date: 07/2022 |
| hg38_45 | Homo sapiens (human) | [Gencode Release 45](https://www.gencodegenes.org/human/release_45.html) | [GRCh38](https://www.gencodegenes.org/human/release_45.html), Annotation Release date: 03/2023 |
| mm10_M21 | Mus musculus (mouse) | [Gencode Release M21](https://www.gencodegenes.org/mouse/release_M21.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M21.html), Annotation Release date: 04/2019 |
| mm10_M23 | Mus musculus (mouse) | [Gencode Release M23](https://www.gencodegenes.org/mouse/release_M23.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M23.html), Annotation Release date: 09/2019 |
| mm10_M25 | Mus musculus (mouse) | [Gencode Release M25](https://www.gencodegenes.org/mouse/release_M25.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M25.html), Annotation Release date: 04/2020 |
| mCalJac1_2021 | Callithrix jacchus (white-tufted-ear marmoset) | [Genome assembly mCalJa1.2.pat.X](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) | Annotation release date: 04/2021 |

You can run `renee run --help` to view the most up-to-date list of genome annotations available in your installation of RENEE.

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