Questions tagged [rna]

Use this tag to refer questions that are related to rna sequence.

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about the scaling after normalization and transformation in RNA-seq data

When we use count data in RNA-seq analysis, we usually use normalization and sometimes vst, rlog transformation (DESeq2)or log2(CMP+4) transformation (edgeR) to perform K-means clustering. Can we use ...
user224050's user avatar
5 votes
1 answer

How to compute the chance of failing to detect a gene given the detection limit of a protocol

In Shapiro et al., when discussing about loss of molecules as source of error in single-cell sequencing, it is written that: Another source of error is losses, which can be severe. The detection ...
gc5's user avatar
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5 votes
2 answers

Reads mapped to exonic, intronic and intergenic regions

After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason? ...
stack_learner's user avatar
4 votes
3 answers

Expression of a gene in different groups

I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not. From this paper lncRNA ...
beginner's user avatar
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4 votes
1 answer

How to calculate the Maximum Ladder Distance (MLD) of ssRNA from Dot-Bracket notation?

The ladder distance (LD) between residue i and residue j is the minimum number of base pairs (created due to secondary structure of the ssRNA) one has to cross when going from i to j. The Maximum ...
user avatar
2 votes
1 answer

Applying PCA or tSNE on non-numerical data

Reading through this t-sne blogpost and I'm a little unclear on how i'd use either of these algorithms here for my goals. i get it'd cluster my samples based on similarity in terms of first and second ...
joshua213p's user avatar
1 vote
2 answers

How to filter ribosomal RNA from scRNA-seq data

I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA? The only solution I found is SortMeRNA, however it works with raw sequencing ...
gc5's user avatar
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