Questions tagged [rna]
Use this tag to refer questions that are related to rna sequence.
100
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What to use to edit RNA alignments?
I have many alignments from Rfam Database, and I would like to edit them.
I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ?
e....
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3
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How to extract RNA sequence and secondary structure restrains from a PDB file
I'm trying to find a programmatic way to automatically extract the following information from a PDB file:
RNA sequence
Secondary structure restraints in bracket format, e.g. ...
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votes
1
answer
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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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2
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5' and 3' bias in Rna-seq data
I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
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Estimate the length of poly-A tails from randomly-primed RNAseq data
So a poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule.
For my project, I would like ...
- 1,681
5
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1
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Why does the SARS-Cov2 genome has letter t [duplicate]
ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is part of the 5'UTR of genome of an RNA virus SARS-Cov-2.
RNA contains letters ...
- 61
5
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2
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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?
...
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5
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1
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102
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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 ...
- 1,783
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1
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126
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How can I dock a protein to a nucleic acid?
I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.
What tool can I use?
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5
votes
2
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591
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Integrating bulk RNA-Seq data with different sequencing depths and from different sources
I am attempting to integrate different bulk RNA-Seq datasets. While this is not ideal, I'm trying to reduce the technical variability in these datasets by using data generated by similar protocols (...
5
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0
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Parse RNA variant effect annotations ("r." format)
I've got annotations for splicing variants in a format like this (this is one variant):
Variant: NM_004092.3:c.88+5G>A
Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23)
I want to extract ...
- 51
4
votes
1
answer
214
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Why is ribosomal RNA difficult to remove even with Poly(A) selection?
In this answer (actually in a comment), it is stated that:
As you've noticed from your own analysis, the ribosomal genes have quite variable expression across cells. They're expressed everywhere, ...
- 1,783
4
votes
1
answer
79
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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 ...
user36028
4
votes
3
answers
455
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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 ...
- 631
4
votes
1
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420
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Plot to show the expression of genes between tumor and normal
I have RNA-seq raw counts data for 50 samples. 20 Normal and 30 tumor. After differential analysis I got 30 DEGs. I want to make a violin plot showing the expression of each gene. I transformed counts ...
- 631
4
votes
1
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159
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RNA folding at specific temperature with ViennaRNA in python
I am trying to get dot-bracket-notations of single stranded RNA via the ViennaRNA python package (https://pypi.org/project/ViennaRNA/) at different temperatures. I have read in the docs (https://www....
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4
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Basic questions about GSEA
I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, ...
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3
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2
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How to convert featureCounts to FPKM?
I have seen many posts regarding counts to RPKM and TPM. I haven't seen any post for counts to FPKM.
I have RNA-Seq data which is paired-end reads. Extracted the counts using featureCounts for all ...
- 631
3
votes
2
answers
1k
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Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05
I'm using edgeR for differential analysis. Using glmTreat function I'm detecting differentially expressed genes between Tumor and Normal. I have set the arguments like below:
...
- 1,262
3
votes
1
answer
345
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How to select only RNA with Hetero atoms from pdb file with python?
I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
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3
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255
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How to visualize genome track of gene in specific cell-lines?
I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data.
It should look something like this I have recently seen this encode, but in ...
- 1,262
3
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1
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Strange per sequence GC content results
I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination ...
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3
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1
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418
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Why is bulk RNA sequencing reflecting AVERAGE expression but not TOTAL expression of all cells?
When I am reading papers that compares bulk RNA sequencing and single-cell RNA sequencing, we often see papers describe bulk RNA seq measures the average cell expression.
For example, in this paper ...
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3
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Question about Co-expression analysis and finding targets for lncRNAs
I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs)
I wanted to do co-expression analysis between ...
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2
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2
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99
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Which software is used to run Molecular Dynamics simulation of a small RNA hairpin?
I am currently working in a project that needs MD simulation of a small RNA hairpin. I am currently trying it on GROMACS but it seems to be protein based, hence am facing several issues.
Is there any ...
AKV
2
votes
3
answers
374
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Selection of differential expressed genes
I'm working with RNA-seq data. I have 40 tumor samples and 5 Normal samples. Differential analysis with Deseq2 based on Fold change > 1.2 and alpha < 0.05 gave ...
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2
votes
2
answers
39
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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 ...
- 537
2
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1
answer
34
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Real time transcript profiles
Do any methods exist (or are in the process of development) for investigating transcript data without lysing the cells, i.e, destroying the sample?
- 121
2
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1
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35
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rRNA genes missing from metagenomic bins; is there a way to recruit them?
I have a couple of metagenomic bins which are okay in quality, but often missing rRNAs (16S, 23S...). I assume this is due to high population variability, combined with the high conservation of rRNAs, ...
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3
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76
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beginner RNA-seq Replicate papers
have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I would like to try to replicate some Rna-seq analysis with R papers (with ...
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2
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1
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82
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Understanding ViennaRNA RNAdistance scoring table
I'm trying to compare the output of 2 different algorithms of RNA structure prediction
(my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA ...
- 141
2
votes
1
answer
81
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I have used TER to break the long bonds of a chain in my PDB
I’m now not sure what I need to alter in my PDB to get it to work in leap. I know breaking the bonds turns the formerly connected residues into terminal residues.
It keeps saying that 3 of my atoms no ...
user9855
2
votes
1
answer
58
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Protein misfolding
I am looking for literature on protein and RNA mis-folding. I am on the computational/biophysics side, and what interests me are the practical applications: diseases caused by misfolding, drug ...
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2
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2
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291
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Tool for rna/lna melting temperature prediction
Is there any tool available to predict the melting temperature for rna/lna oligos with its perfect complement ?
I know this amazing website from qiagen/geneglobe that estimates the tm value.
But ...
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2
votes
1
answer
65
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How can I interpret gene expression data from Bioconductor packages?
I am currently looking at microarray data from a bioconductor microarray dataset. Specifically, I have data (a snippet) which looks like the following:
...
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2
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1
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374
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How to get rid of the temp files while using "featureCounts" for extracting readcounts from bam files?
I used this command for extracting read counts for almost 60 samples using featureCounts.
...
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2
votes
2
answers
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Sequence Alignment for sequences with the same length
I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
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2
votes
1
answer
36
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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 ...
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2
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1
answer
70
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Is there a graphical/interactive 16S rRNA clustering method?
I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.
Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
- 881
2
votes
1
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167
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How does FDRtool work?
I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired using Deseq2), the FDRtool was first used and thereafter p.adjust using the benjamini hochberg ...
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2
votes
1
answer
44
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Simple Affy Differential Expression
I think I have a fairly easy-to-solve problem.
I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total.
So I ...
- 401
2
votes
1
answer
32
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Help with finding an unsupervised learning algorithm for RNA sequence/structure pattern identification
I have a bunch of RNA sequences (and their optimal secondary structures) and their corresponding energy values (measured by mean free energy) and I'm trying to find a way to identify features (...
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2
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0
answers
264
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ExecutiveAlign error: atomic alignment failed (mismatched identifiers? )
So I have a molecule (a dsRNA) , that has two conformations. I want to align it in pymol with molecules but I get the following error: ExecutiveAlign error: atomic alignment failed (mismatched ...
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2
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0
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90
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Adapter trimming
I am trying to do adapter trimming, alignment and sorting for a range of large scale paired end fastq files. The code I am using is given below:
...
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2
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0
answers
48
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Explaining the algorithm of RNA folding: what each symbol & value represents?
I need someone to explain to me from the nuts and bolts how algorithms/ maths is used to work out RNA folding. Explain it to me like I am an alien or child.
I am looking at this paper - https://eprint....
2
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0
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123
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How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA
In the tutorial of RNAfold it states,
RNAfold reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in ...
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2
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6k
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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 ...
- 1,783
1
vote
2
answers
754
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Why the t-test for a specific gene shows different value compared to differential analysis?
I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR.
With a FC > or &...
- 631
1
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1
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199
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Gene symbol list for all protein coding genes in mice
How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess ...
- 376
1
vote
2
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105
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Basic RNA Differential Expression in R
I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression.
...
