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Questions tagged [rna]

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

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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 ...
Ron's user avatar
  • 51
2 votes
0 answers
350 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 ...
majumderS's user avatar
2 votes
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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: ...
Aranyak Goswami's user avatar
2 votes
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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....
confused_novice's user avatar
2 votes
0 answers
138 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 ...
aerijman's user avatar
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1 vote
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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 ...
K_081's user avatar
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1 vote
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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 ...
Rachel Sweeney's user avatar
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 ...
joshua213p's user avatar
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.
julierebecca's user avatar
1 vote
0 answers
192 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 ...
user224050's user avatar
1 vote
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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. ...
MudithMMBc's user avatar
1 vote
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145 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 ...
Tain Luquez's user avatar
1 vote
0 answers
302 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 ...
L R Joshi's user avatar
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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.
majumderS's user avatar
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97 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 ...
Serij's user avatar
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1 answer
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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/...
Gojih's user avatar
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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 ...
user14648's user avatar
-1 votes
1 answer
302 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 ...
hepcat72's user avatar
  • 221