Questions tagged [rna-splicing]

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2
votes
3answers
83 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 ...
6
votes
1answer
635 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....
2
votes
2answers
187 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
votes
2answers
127 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
votes
2answers
93 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 ...
1
vote
3answers
143 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
votes
1answer
49 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
votes
1answer
167 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
votes
1answer
252 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 ...
4
votes
1answer
61 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
votes
2answers
391 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 ...