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I was just wondering if anyone knew which GTF file I should be using for my AS analysis.
I'm using mapped BAM files that I've aligned to a Glycine max reference genome.
However, If I'm doing alterna…
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Dear,
We succesfully implemented CTAT-splicing in our STAR-fusion pipeline.
**1) we pick up all our relevant fusion genes using STARfusion**
**2) we correctly picked up METx14del,** without fal…
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I tested SPLASH with a couple of samples, however I am not sure that I understand the correct way to proceed when having an specific experimental design. In my case, I have 2 types of samples, one set…
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> - Motivation
Alternative splice site selection is inherently competitive and the probability of a given splice site to be used also depends on the strength of neighboring sites. Here, we present a …
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Hi there,
Thanks for the wonderful new tools! I have a question about the output of the script [new_annotator_with_skipping.py](https://github.com/landau-lab/ONT-sc-splice/blob/main/junction_annota…
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would be epic
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Currently we compare peptide sequences against a reference proteome from Ensembl.
It would be more correct to create a proteome that incorporated SNPs that impact protein sequence and then look f…
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I realized that I will be working with a very large number of samples representing data from over 20 conditions. The paper mentions - "PsiCLASS is designed to leverage the gene information across samp…
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Thank you for providing an interesting tool for analyzing alternative splicing. When conducting SJ position analysis, no transcripts were identified, even different genes. Here is our code and results…
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I'm trying to use STAR to align RNA-seq data to HPV16 genome. My main goal is to analyze alternative splicing. Because HPV16.gtf only contains CDS not exon, I change all CDS into exon. However, there …