Questions tagged [rna]
Use this tag to refer questions that are related to rna sequence.
84
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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 ...
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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 ...
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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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Is there a software that extract molecular descriptors of single stranded RNAs secondary structure from dot bracket notation in nucleotide resolution?
I want to generate descriptors from dot bracket notations of single stranded RNA/DNA secondary structures. So far i have come across this paper:https://journals.plos.org/plosone/article?id=10.1371/...
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Is it possible to create SMILES representation out of DNA/RNA-Oligonucleotides (~50 nts)?
I want to use physico chemical descriptors of single stranded DNA/RNA-Oligonucleotides in order to model certain properties. To generate these descriptors i need a computer understandable ...
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Is there a tool to visualize RNA secondary structure?
I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures.
I haven't found a single program that does that.
thanks
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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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Is current AI able to generate RNA sequences of viruses? [closed]
After seeing a video of a combination of CRISPR and AI, and an article of someone who made two babies immune against HIV and still healthy, I wondered about something. If such complicated thing, to ...
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Visualize RNA co-folded secondary structure with Python
I would like to visualize the secondary structure of co-folded RNA strands in Python, preferably in a Jupyter notebook.
What are the recommended tools? Can anyone provide an example?
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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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Is loss/gain of function reflected in RNA-seq transcript counts?
Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
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Expression analysis of miRNAs with normal RNA-seq data without small RNA-seq data
I am looking to perform expression analysis of miRNAs with normal RNA-seq data lacking small RNA-seq data?
Which path should I choose for known miRNAs and unknown new miRNAs?
Data set: rna-seq data ...
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Transcriptome analysis
I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
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RNA strings and amino acid string
Which of the following RNA strings could translate into the amino acid string PRTEIN? (Select all that apply.)
I am not sure if the following mass of amino acid is relevant to the question.
...
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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.
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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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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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Pipeline for paired end RNA sequence data to proteins
Forgive the basic question here, but I'm super novice at this ...
I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and ...
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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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Error generating count data using featurecounts in R
I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
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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 ...
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What is meant by transcriptional changes executed by the cell over a time period?
I read the following line in the research paper - The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells:
During differentiation, for example, each ...
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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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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 ...
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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 ...
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How to count RNA sequencereads using custom made python scripts?
I am trying to do RNA seq analysis and my goal is to filter gene counts less than 5 using custom made python scripts. The code chunk goes as follows
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Is is possible to predict ncRNAs from sequence and homology alone?
I'm working with a set of homologous genes (let's call it gene A) from several bacterial species.
I know (from previously published research) that in gene B (a close paralogue of gene A), there is a ...
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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
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177
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Are codons in RNA layered? Are we misinterpreting RNA codons?
I am analyzing nucleotide base-pair patterns in RNA and DNA, and had a thought about RNA and DNA (Let me first state though, I am not a biologist; I am an algorithmatician, employing a sort of ...
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smallest length of reads in 3'quantseq?
I am studying about RNA seq, and especially about 3'Quantseq(tagseq, 3primeseq). I wonder if there is a cutoff for the reads length. By this I mean that given that 3'quantseq targets the end of the ...
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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....
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Bacterial DNA at the tail of transcriptome reads. What does that mean?
I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
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197
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RNA seq .counts.txt to bigwig conversion
I've downloaded neuronal RNA seq data from GEO. The files are in .counts.txt format. Could I convert them to bigwig? If so, how?
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389
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about the cpm normalization after using normalization factor
Is it okay to use CPM normalization (with/without log transform) after using TMM normalization? Why do we need both?
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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 ...
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about the normalization of RNAseq data for calculating distance for unsupervised learning
I have been working on clustering using RNAseq data. To compute distance, what kinds of normalization is optimal?
Can we use normalization using relative log normalization? I understand this should ...
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How to understand and analyse RNA-seq data (for a beginner)?
I am trying to understand expression of a certain protein across Pseudomonas species. I downloaded an SRA file from NCBI and converted it to a fastaq file. I am not able to understand how to interpret ...
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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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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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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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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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What are the meanings of these transcript ids?
I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser.
...
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WGCNA: Problem with selecting soft threshold
I have 25 tumor samples with counts data. Initially, I filtered out low expressed genes and then converted counts to varianceStabilizingTransformation using ...
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Writing a python module to run Infernal on a list of fasta files
I am very new to using python3 and am hoping to use it to reduce the time I need to spend running Infernal to look for a variety of RNAs in a large collection of bacterial genomes. I am hoping to ...
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how to calculate coverage of each base of mapped reads?
I have a RNA aligned file without any header info.
I need to calculate the coverage of each mapped base for per chromosome. Is it possible to do it with perl ?
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Arm-level SCNA does not change mRNA expression level?
It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA ...
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How to handle control samples in CLIP-Seq
I have a CLIP-Seq dataset I'm processing, which includes control samples and no inputs. This is the second CLIP analysis I've performed to help out users of our genome core facility and the first one ...
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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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Deep learning RNA sequences
Currently I'm working on a project, which combines deep learning with RNA sequences. I'll try to predict pseudotorsion angles [1] from raw rna sequence. The ideas is to train a neural network with raw ...
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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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