Questions tagged [rna]
Use this tag to refer questions that are related to rna sequence.
89
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Getting VCF file that contain common SNPs from 6 VCF file using isec
I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command
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How to analyze hashtagged data with scanpy?
I used hashsolo to demultiplex my data and I am a bit confused as to how to continue the analysis.
Following hashsolo my samples look like below:
...
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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 (...
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How can I calculate the Maximum Ladder Distance (MLD) of ssRNA from Dot-Bracket notation? [duplicate]
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 ...
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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
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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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57
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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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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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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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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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54
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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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