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Hello,
I wanted to try '5_utr_seq_similarity' and '3_utr_seq_similarity' in consequencesToAnalyze for analyzeSwitchConsequences but it raised this error:
```
Step 1 of 4: Extracting genes with iso…
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Hello,
I have run into a problem in part 1 of the analysis, specifically addORFfromGTF. When i try to break down part1 into the component steps I run in to same problem. I had been actively running t…
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Hi,
I used IsoformSwitchAnalyzeR to perform isoform differential analysis and alternative splicing.
I was able to predict alternative splicing, but when I tried to perform consequence analysis I e…
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I have been working with data that I first mapped with HISAT2 then did my alignment, merge, and quantification with StringTie. When I try to use addORFfromGTF I get an error saying there isn't any CDS…
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I wanted to generate venn diagrams from the vignette on the following list:
`asl2`
>This switchAnalyzeRlist list contains:
1612 isoforms from 301 genes
6 comparison from 4 conditions (in total…
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Hi,
I have a switchAnalyzeRlist object and I would like to know what these tables are and what the columns mean. Is this explained somewhere?
```
> isa
This switchAnalyzeRlist list contains:
…
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- Colla…
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Hi,
Fragpipe v16/msFragger v3.3 appears to identify at least one peptide as unique when it is, in fact, not. The peptide, IQLWDTAGQER, is shared among many proteins in the Rab family; for some reas…
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My transcripts have no signal peptides
`grep YES signalP4_prediction_standardTM.txt | wc`
0 0 0
`grep NO signalP4_prediction_standard.txt | wc`
182 910 10815
so when I ru…
mdeea updated
2 years ago
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Hi
This is more of a recommendation than an issue. I'm really interested in intron retention and exon skipping for my research and I find it a bit confusing how this analysis is set up in swanvis now…
rsalz updated
2 years ago