Questions tagged [rna]

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

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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 answers
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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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5 votes
1 answer
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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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-1 votes
1 answer
27 views

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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2 votes
1 answer
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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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1 answer
42 views

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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1 answer
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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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1 answer
26 views

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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1 vote
2 answers
168 views

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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0 votes
1 answer
28 views

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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2 votes
0 answers
44 views

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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1 vote
2 answers
95 views

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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0 votes
1 answer
118 views

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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1 answer
226 views

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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0 answers
140 views

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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0 votes
1 answer
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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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0 votes
1 answer
46 views

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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2 votes
1 answer
56 views

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 votes
2 answers
38 views

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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8 votes
1 answer
142 views

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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3 votes
1 answer
60 views

Practical use of RNA structure

I have spent some time studying RNA structures. While there is a range of interesting phenomena and functions that certainly deserve understanding from the scientific point of view, I have never ...
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2 votes
2 answers
132 views

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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1 vote
0 answers
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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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0 votes
1 answer
1k views

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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1 vote
1 answer
84 views

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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1 vote
1 answer
39 views

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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0 votes
1 answer
23 views

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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-1 votes
1 answer
214 views

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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  • 189
3 votes
1 answer
227 views

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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1 vote
3 answers
309 views

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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2 votes
0 answers
85 views

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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0 votes
1 answer
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I need some tips and suggestions for further analysis of NGS expression data (log2cpm)

I am a PhD student who inherited some log2cpm data of expression data from bulk kidney tissue from a UUO(unilateral urethral obstruction) experiment that tests a new drug. The sample material consists ...
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1 vote
2 answers
62 views

Retrieve RNA sequencing data for human p53 colon cancer cell lines

I want to download the next generation RNA sequencing data in different cell lines. I want the data (alongwith normal) for p53 wild type, p53 knock-out and p53 null cell lines (human colon cancer). ...
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2 votes
3 answers
239 views

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 votes
1 answer
60 views

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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0 votes
3 answers
82 views

Building RNAz on MacOS

Having trouble building RNAz 2.1 on MacOS. Following instructions at https://www.tbi.univie.ac.at/software/RNAz/ ...
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2 votes
2 answers
64 views

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 ...
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2 votes
1 answer
30 views

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?
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1 vote
2 answers
472 views

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 &...
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3 votes
2 answers
5k views

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 ...
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  • 621
1 vote
0 answers
114 views

How to correctly parallelise RSeQC scripts with GNU parallel?

I have a .bam, as ouput from STAR aligner, from which I need to extract some info using RSeQC while using all the computational resources available to increase ...
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3 votes
2 answers
142 views

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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4 votes
1 answer
332 views

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 ...
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  • 621
2 votes
3 answers
278 views

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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  • 621
1 vote
1 answer
2k views

How to calculate logCPM across all samples?

Using edgeR for differential analysis between Tumor and Normal gave me differential expressed genes with logFC, logCPM, PValue and FDR. From the details of glmTreat function I see that logCPM is ...
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