Run RNA-seq pipeline using the Telomere-2-Telomere (T2T) latest human genome
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies (Nurk et al., Science, 2022 https://www.science.org/doi/10.1126/science.abj6987).
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GCF_009914755.1_T2T-CHM13v2.0_assembly_report.txt GCF_009914755.1_T2T-CHM13v2.0_genomic.fna GCF_009914755.1_T2T-CHM13v2.0_genomic.gff GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf GCF_009914755.1_T2T-CHM13v2.0_protein.faa GCF_009914755.1_T2T-CHM13v2.0_rna.fna |
Print the assembly report:
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cat /work/training/references/ncbi/T2T/GCF_009914755.1_T2T-CHM13v2.0_assembly_report.txt |
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# Assembly name: T2T-CHM13v2.0
# Description: T2T CHM13v2.0 Telomere-to-Telomere assembly of the CHM13 cell line, with chrY from NA24385
# Organism name: Homo sapiens (human)
# Taxid: 9606
# BioSample: SAMN03255769
# BioProject: PRJNA559484
# Submitter: T2T Consortium
# Date: 2022-01-24
# Assembly type: haploid
# Release type: major
# Assembly level: Complete Genome
# Genome representation: full
# Expected final version: no
# Genome coverage: 30x
# GenBank assembly accession: GCA_009914755.4
# RefSeq assembly accession: GCF_009914755.1
# RefSeq assembly and GenBank assemblies identical: no
#
## Assembly-Units:
## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name
## GCA_009914825.4 GCF_009914825.1 Primary Assembly
## GCA_009914855.2 non-nuclear
#
# Ordered by chromosome/plasmid; the chromosomes/plasmids are followed by
# unlocalized scaffolds.
# Unplaced scaffolds are listed at the end.
# RefSeq is equal or derived from GenBank object.
#
# Sequence-Name Sequence-Role Assigned-Molecule Assigned-Molecule-Location/Type GenBank-Accn Relationship RefSeq-Accn Assembly-Unit Sequence-Length UCSC-style-name
1 assembled-molecule 1 Chromosome CP068277.2 = NC_060925.1 Primary Assembly 248387328 chr1
2 assembled-molecule 2 Chromosome CP068276.2 = NC_060926.1 Primary Assembly 242696752 chr2
3 assembled-molecule 3 Chromosome CP068275.2 = NC_060927.1 Primary Assembly 201105948 chr3
4 assembled-molecule 4 Chromosome CP068274.2 = NC_060928.1 Primary Assembly 193574945 chr4
5 assembled-molecule 5 Chromosome CP068273.2 = NC_060929.1 Primary Assembly 182045439 chr5
6 assembled-molecule 6 Chromosome CP068272.2 = NC_060930.1 Primary Assembly 172126628 chr6
7 assembled-molecule 7 Chromosome CP068271.2 = NC_060931.1 Primary Assembly 160567428 chr7
8 assembled-molecule 8 Chromosome CP068270.2 = NC_060932.1 Primary Assembly 146259331 chr8
9 assembled-molecule 9 Chromosome CP068269.2 = NC_060933.1 Primary Assembly 150617247 chr9
10 assembled-molecule 10 Chromosome CP068268.2 = NC_060934.1 Primary Assembly 134758134 chr10
11 assembled-molecule 11 Chromosome CP068267.2 = NC_060935.1 Primary Assembly 135127769 chr11
12 assembled-molecule 12 Chromosome CP068266.2 = NC_060936.1 Primary Assembly 133324548 chr12
13 assembled-molecule 13 Chromosome CP068265.2 = NC_060937.1 Primary Assembly 113566686 chr13
14 assembled-molecule 14 Chromosome CP068264.2 = NC_060938.1 Primary Assembly 101161492 chr14
15 assembled-molecule 15 Chromosome CP068263.2 = NC_060939.1 Primary Assembly 99753195 chr15
16 assembled-molecule 16 Chromosome CP068262.2 = NC_060940.1 Primary Assembly 96330374 chr16
17 assembled-molecule 17 Chromosome CP068261.2 = NC_060941.1 Primary Assembly 84276897 chr17
18 assembled-molecule 18 Chromosome CP068260.2 = NC_060942.1 Primary Assembly 80542538 chr18
19 assembled-molecule 19 Chromosome CP068259.2 = NC_060943.1 Primary Assembly 61707364 chr19
20 assembled-molecule 20 Chromosome CP068258.2 = NC_060944.1 Primary Assembly 66210255 chr20
21 assembled-molecule 21 Chromosome CP068257.2 = NC_060945.1 Primary Assembly 45090682 chr21
22 assembled-molecule 22 Chromosome CP068256.2 = NC_060946.1 Primary Assembly 51324926 chr22
X assembled-molecule X Chromosome CP068255.2 = NC_060947.1 Primary Assembly 154259566 chrX
Y assembled-molecule Y Chromosome CP086569.2 = NC_060948.1 Primary Assembly 62460029 chrY
MT assembled-molecule MT Mitochondrion CP068254.1 <> na non-nuclear 16569 chrM |
Run RNAseq pipeline using a custom genome
We can use the nf-core/rnaseq pipeline to profile the expression of genes in a custom genome (e.g., T2T or any animal or plant genome) of your interest, as long as there is a reference genome (FASTA file) and genome annotation (GTF or GFF3).
To use your own genome assembly - you need 1) FASTA genome sequence and 2) GFF/GTF genome annotation file
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--fasta my_custom_genome.fasta # de novo assembled genome or genome not available as an igenomes reference --gtf my_custom_genome.gtf # genome annotatio showing the location of genes |
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cp /work/training/2024/rnaseq/data/human/samplesheet.csv $HOME/workshop/2024-2/session4_RNAseq/runs/run3_RNAseq_T2T cp $HOME/workshop/2024-2/session4_RNAseq/scripts/launch_nf-core_RNAseq_pipeline_T2T.pbs $HOME/workshop/2024-2/session4_RNAseq/runs/run3_RNAseq_T2T |
Line 1: Copy the samplesheet.csv for pre-downloaded human samples file to the working directory
Line 2: Copy the launch scrip to run expression profiling using the T2T genome
Print the content of the “launch_nf_core_RNAseq_T2T.pbs” script:
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qsub launch_nf_core_RNAseq_T2T.pbs |
Tip: Read the help information for Nextflow pipelines
Information on how to run a nextflow pipeline and additional available parameters can be provided on the pipeline website (i.e., https://nf-co.re/rnaseq/3.12.0/docs/usage/ ). You can also run the following command to get help information:
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