Questions tagged [rna]
Use this tag to refer questions that are related to rna sequence.
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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 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 ...
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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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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 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 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 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 ...
M__♦
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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 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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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 ...
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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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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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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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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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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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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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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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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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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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How to create a SAF file for virus sequence?
I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by featureCounts. I need to create my own SAF. I ...
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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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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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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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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 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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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 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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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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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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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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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 ...
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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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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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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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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:
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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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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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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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