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Hi, If I only need to obtain the AS count for a single sample (experimental group or control group), I execute this command: rmats.py --b1 b2.txt --gtf isoquant_gffcompare.gtf -t paired --bi ./STAR_bi…
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How to keep channel state during the splicing process?
Several alternatives:
- Add a few fields (new struct member to `channel.pending_splice`), and keep splicing state there (items such as new ca…
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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…
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First and foremost, I would like to thank you for developing the fantastic DIA-NN tool.
I am currently working on a project where I aim to distinguish and quantify isoforms produced by alternative …
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Dear author,
There is an error in my running, how should i solved it?
```
ValueError: can only convert an array of size 1 to a Python scalar
running: ['miniconda3/envs/rMATS-long/bin/python', 'min…
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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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Question 1
In my case of using rMATs. Too many MXE events in >80% samples (see attached). I also found most differentially expressed splicing events were MXE. Did these reasonable?
[AS_sample_number…
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For example, in case of alternative splicing, exons shared between isoforms can either be 1) duplicated or 2) have multiple `Parent` values.
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Hello,
I am using briekit-events to extract splicing events from the human gencode v25 annotation file in gff3 format, which has over 55k genes. However, the output file has alternative splicing ev…
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Hello,
I'm analysing single-cell full-length RNA sequencing data. I would like to perform an analysis on alternative splicing exons, which has been mentioned multiple times in your research group's…
weib3 updated
5 months ago