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Funannotate final gff3 has only one transcript information per gene. It doesn't provide alternative splicing/isoforms in the gff file?
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Hello rMATS community,
I'm new to alternative splicing (AS) analysis and seeking guidance on a few topics. Any help would be greatly appreciated!
1) When running a paired analysis with the --paire…
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Hello,
I recently started to use ASpli to quantify the alternative splicing levels of my gene. My gene has 3 isoforms which only differ from each other by one exon.
- The first one has all exons…
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**Is your feature request related to a problem? Please describe.**
When slicing multiple parts it is possible to override settings on a per part basis.
My Idea is to set an entire Print profile for …
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When I use STAR alone to align reads from two Fastq files, the alignment rate reaches 90%. However, when I use rMATS, the alignment rate is 0%, resulting in no output of any alternative splicing event…
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Hello @EricKutschera,
is there a way to do this `classify_isoform_differences.py` for all isoforms? not doing individually for each isoform so that I have at the end all isoform in a single tsv fi…
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hello,
Thank you for your detailed codes. However I got a question.
I'd like to know if I can directly get which alternative splicing event is annotated in the gtf according to the output files?
If…
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Dear developers,
I have tried JunctionSeq in my project (RNA-Seq-based analysis of alternative splicing during plants development ). JunctionSeq is really a useful tool with powerful visualisation …
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See proposal in the following paper, section "A Flexible Code for Alternative Splicing Events":
> Sammeth, M., Foissac, S., & Guigó, R. (2008). A General Definition and Nomenclature for Alternative S…
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I wanted to create a gtf file having columns
chromosome No., Start, end, gene ID, Strand
and using the GTF file as input for differential expression gene analysis using DESeq2 software.
How s…
nip4n updated
11 months ago