Questions tagged [rna-splicing]

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rMATS and SUPPA on long read sequences?

Has anyone in the community used rMATs or SUPPA for differential splicing analysis in long read data? I have tried using SUPPA2 in PacBio Isoseq + MinION RNA-seq data and can identify the differential ...
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25 views

Do I need to study alternative splicing and isoformswitch separately?

I have done a study on isoform switch between different tissue type. Now, many people asking me to study alternative splicing also. But, dont they will give me same results? If there is a significant ...
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12 views

Logit-normal distribution to model variation among biological replicates

I came across rMATS while doing research on differential alternative splicing (AS). It uses logit-normal distibution to model variation among biological replicates. I am having difficulty ...
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32 views

Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?

I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to ...
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128 views

Coronavirus RNA structures?

Is there anything known about the RNA structures of coronaviruses? More specifically - do they have any interesting known structures in the translatable region, like RRE of HIV or the double loops in ...
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1answer
41 views

Practical use of RNA structure

I have spent some time studying RNA structures. While there is a range of interesting phenomena and functions that certainly deserve understanding from the scientific point of view, I have never ...
2
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3answers
90 views

Calculating p-value for introns which are retained (or not) between 2 conditions

I am trying to calculate p-values and ultimately FDR values for RI introns for 2 conditions of experiment I have(control and knockdown) For every condition I have 3 biological replicates each: 3 ...
9
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1answer
1k views

What are “split reads” and “intron clusters?”

I'm working through the example data set for LeafCutter and the documentation mentions "split reads": This will cluster together the introns fond [sic] in the junc files listed in test_juncfiles....
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2answers
233 views

RNA velocity: competing explanations for variable ratio of spliced to unspliced transcript

In "RNA velocity of single cells", La Manno et al. look at ratios between spliced and unspliced mRNA as a way of estimating the velocity of a cell through transcriptome space. In checking for a ...
4
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2answers
166 views

Exon-exon junctions: compare experimental transcripts to reference annotation

My aim is to parse an experimental transcript set (obtained by RNAseq) to check which splice junctions are already reported in a reference annotation and which ones are new. I tried ...
3
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2answers
107 views

Detect transcript isoform abundance for a specific gene in scRNA-seq

I want to detect the count of isoform transcripts for a specific gene in scRNA-seq data. Data is coming from cells of Mus Musculus. For transcript isoforms I mean the different alternatives provided ...
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153 views

Intron retention events for a condition sample with 3 replicates

I have 3 biological replicates of RNA seq data for a particular condition. I want to find out intron retention events from those biological replicates for a given condition. There is no comparison I ...
2
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1answer
57 views

How can I find out the code DRIMSeq uses to make dmplotProportions objects?

I'm using DRIMSeq to do some analysis but I'd like to make my own figures from the results ideally using what they've done as a base. I'm trying to find how they make their ggplot objects in the ...
8
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1answer
187 views

Convert local alignments to spliced alignments in SAM file

I mapped RNA reads to reference genome, using LAST in split mode, and converted the MAF alignment to SAM with maf-convert. My problem is that the transcripts are not reported in a spliced manner, ...
4
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1answer
325 views

insert size pre and post trimming

I have a problem here with my rna seq data: Sequencing details: rRNA was removed, followed by cDNA preparation and generation of stranded libraries using the TruSeq Stranded Total RNA Sample Prep Kit. ...
4
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1answer
64 views

How to represent trans-spliced genes in GTF?

For example, see this gene (nad1) in ENA: http://www.ebi.ac.uk/ena/data/view/ABI60879 If you look at the XML for that gene you see the following: ...
7
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640 views

Spliced vs. unspliced ratios for transcripts in RNA-seq data

Is there a computational tool for measuring what percentage of RNA is spliced in an RNAseq experiment? I'm not particularly interested in complicated analyses that give ratios for all possible ...