Comments (3)
Hi! The GTF is the common format that you can use as input. It does not have to be generated from TALON!
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Thanks for your prompt reply. Sorry if I've misunderstood as I'm new to this. To my knowledge, a gtf file usually refers to the annotation gtf file, which has already been supplied in the previous step via sg.add_annotation(annot_gtf). I downloaded mine from Ensembl (https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/). May I know what this transcriptome gtf is and where else can I obtain? coz I don't seem to see any other GTF-formatted file from my pipeline outputs. Thanks so much!
from swan_vis.
Ah I see. If you are not doing transcript discovery in your data processing, you don't need to add another transcriptome GTF file, as all of the transcript that you're detecting are already from the Ensembl GTF you've mentioned. This is a characteristic I'd expect from a short-read RNA-seq data processing pipeline, am I correct in assuming this? If you are using long-read RNA-seq data, what are you using to process it?
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Related Issues (20)
- swanvis broken? HOT 3
- Intron retention and exon skipping analysis HOT 22
- Missing transcripts HOT 3
- AttributeError: 'SwanGraph' object has no attribute 'ass_transcriptome' HOT 2
- replace talon.db HOT 10
- plot a transcript with all transcripts as background HOT 8
- relation between splicing in/out sites and exons HOT 5
- Issues differential expression HOT 3
- Differential isoform usage multiple conditions HOT 1
- find_es_genes returns duplicated entries
- Example code problem HOT 1
- MemoryError: Unable to allocate 113. GiB for an array with shape (9992, 3033596) and data type float32 HOT 5
- Switch diffexp to pydeseq2 for differential gene and transcript expression testing HOT 1
- Index contains duplicate entries, cannot reshape HOT 4
- sg.add_adata(adata_file) not working HOT 5
- Speeding up Exon skipping and intron retention on HPC
- ES IR error HOT 10
- Missing case for plottedgraph init HOT 2
- Novelty info not found HOT 3
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