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Hi,
Could you explain the content of prep .rmats file? I want to do some intermediate summary, like how many reads from the bam were utilized to support the overall AS event. Thanks for your help.
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Current SBOL RNA-related glyphs (i) do not capture the range of RNA functions and (ii) where they do exist are not expressive enough to precisely annotate the RNA function. A new set of glyphs that mo…
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Hi,
I am getting some error when running Whippet-index.jl, where it complains that it is out of bounds, even though it should still be within the the reference genome:
```
julia Whippet.jl/bin/w…
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Hi, I am trying to run loftee on Linux. Below is my command and error message.
Can someone please kindly let me know what is wrong here?
Thank you & best regards,
jie
=== my command ===
v…
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hi ,there
The scallop is a good software to assembly the illumina data and I got lots of transcripts that other softwares can not. When I use the ORFfinder to predict the ORF with the scallop resu…
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Hi again,
I would like to know if the number of times a circRNA is repeated in each read (which I think you call CCS copy number) is reported somewhere in the output of CIRILONG. Mi idea is to get …
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I'm using `scoreSeq5` and `scoreSeq3` to generate scores for a few sequences from Ensembl. How do I interpret the output scores in terms of splice-sites (acceptor/donor)?
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Hi,
I wanted to use AS-Quant for checking how splicing is affected. But the code gives me this kind of error! Until this point, everything was looking fine! I have 3 replicates in each folder! What …
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Hello, I am following the pipeline of finding alternative splicing analysis using QoRTs and JunctionSeq.
I am working on tomato rna-seq data
I have used HISAT2 for alignment and used "--minMAPQ 60".…
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Enjoying the great tool, but I have another question:
One of my sample had following stats of used and unused reads (following the 2-pass alignment strategy with STAR)
read outcome totals across a…