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Questions tagged [rna]

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

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1 vote
1 answer
41 views

What algorithm should I use to find what RNA sequence/structural elements lead to different labelled MFE values?

To put it super simply: I have RNA sequences, their optimal secondary structures, and the MFE values of those structures. I'm trying to computationally identity what structural elements and/or ...
2 votes
1 answer
21 views

Is there a database of oligonucleotide duplex sequences and their melting temperatures

I am looking for melting temperatures of oligonucleotide duplexes, but I am having trouble finding data. Can be DNA-DNA, DNA-RNA, or RNA-RNA duplexes, native or modified nucleotides.
0 votes
1 answer
15 views

Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset

I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my ...
1 vote
0 answers
26 views

Is it normal to have low mapping to bacterial genome in a total RNA sample of plant root-colonized bacterial cells?

I had isolated the total RNA from a sample of plant roots with colonized bacteria by excising the roots (harboring the bacterial cells) and crushing them into a powder using liquid nitrogen. The RNA ...
0 votes
1 answer
63 views

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/...
1 vote
1 answer
73 views

issue with rna seq analysis

I am working on RNA seq analysis and I would like to know the following things: Current Methods: downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 performed ...
2 votes
2 answers
73 views

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 ...
1 vote
0 answers
25 views

What are some good miRNA databases?

I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein ...
0 votes
1 answer
168 views

HISAT2: RNA strandedness

My library is unstranded and the code I'm trying to use is this: ...
1 vote
1 answer
97 views

Would DESeq2 be appropriate or should I use another tool for differential gene expression?

Hay, this question is sort of an extension of previous post. We have sequenced extra cellular RNA from culture media. Since the number of cells were limited, we did not have enough material for ...
0 votes
0 answers
30 views

Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?

Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.
0 votes
0 answers
95 views

What is happening in the Zuker-Algorithm

I am trying to understand the Zuker Algorithm. What is happening during initialisation? I know in Nussinov the diagonal is filled with 0s. Are the diagonals filled with infinite energy during Zuker´s ...
1 vote
2 answers
3k 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 ...
2 votes
1 answer
77 views

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 ...
2 votes
1 answer
35 views

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 (...
2 votes
1 answer
54 views

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 ...
0 votes
2 answers
1k views

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. ...
1 vote
1 answer
40 views

How do I fix this limma line?

I'm trying to conduct lmFit on my fread::table matrix: ...
1 vote
1 answer
242 views

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 ...
0 votes
1 answer
263 views

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: ...
5 votes
2 answers
955 views

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 votes
1 answer
124 views

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 ...
1 vote
1 answer
322 views

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 ...
2 votes
1 answer
318 views

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 ...
2 votes
0 answers
340 views

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 ...
0 votes
2 answers
179 views

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
4 votes
1 answer
181 views

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....
1 vote
1 answer
99 views

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 ...
3 votes
3 answers
285 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 ...
1 vote
1 answer
384 views

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?
2 votes
0 answers
92 views

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: ...
0 votes
1 answer
69 views

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?
1 vote
1 answer
74 views

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 ...
1 vote
0 answers
31 views

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.
1 vote
2 answers
106 views

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. ...
2 votes
1 answer
36 views

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, ...
2 votes
3 answers
79 views

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 ...
1 vote
1 answer
75 views

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 ...
0 votes
1 answer
80 views

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 ...
2 votes
2 answers
321 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 ...
5 votes
0 answers
53 views

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 ...
2 votes
0 answers
48 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....
1 vote
0 answers
300 views

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 ...
3 votes
1 answer
453 views

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 ...
5 votes
1 answer
88 views

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 ...
0 votes
0 answers
150 views

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 ...
-1 votes
1 answer
30 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 ...
-1 votes
1 answer
298 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 ...
0 votes
1 answer
27 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 ...
2 votes
1 answer
200 views

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 ...