Questions tagged [rna]

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

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14 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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1answer
36 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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38 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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1answer
37 views

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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1answer
38 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 ...
2
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1answer
38 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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0answers
22 views

How to find the region with frequent mutation?

I am very new to bioinformatics and I was wondering if I can get some help regarding finding region that has high mutation rate. Currently, I have 2 fasta files, one that is aligned and one regular ...
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2answers
30 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 ...
2
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1answer
78 views

Coronavirus phylogeny and evolution

This new article presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it ...
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1answer
123 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 ...
3
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1answer
40 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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1answer
22 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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0answers
24 views

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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0answers
33 views

Simulating RNA Editing

I'm pretty new to bioinformatics and I have been looking for a way to simulate rna sequencing with editing, specifically A to G, but didn't find anything i could use. I tried using flux simulator but ...
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1answer
191 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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1answer
50 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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1answer
34 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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0answers
92 views

Zuker RNA Folding Traceback Algorithm

I am trying to re-implement Zuker's algorithm for RNA Folding, which considers free energy minimization rather than number of possible pairs in Nussinov's algorithm. I understand how to populate the ...
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0answers
15 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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1answer
73 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 ...
3
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1answer
85 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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3answers
224 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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0answers
57 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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1answer
60 views

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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2answers
58 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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3answers
204 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 ...
2
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1answer
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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3answers
69 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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2answers
50 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 ...
2
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1answer
27 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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2answers
163 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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2answers
3k 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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0answers
67 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 ...
2
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0answers
58 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 ...
4
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1answer
181 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 ...
2
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3answers
180 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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1answer
1k 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 ...
3
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2answers
179 views

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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0answers
72 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 ...
4
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3answers
295 views

Expression of a gene in different groups

I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not. From this paper lncRNA ...
5
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2answers
495 views

Reads mapped to exonic, intronic and intergenic regions

After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason? ...
2
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1answer
100 views

How to get rid of the temp files while using “featureCounts” for extracting readcounts from bam files?

I used this command for extracting read counts for almost 60 samples using featureCounts. ...
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2answers
293 views

What could be the reason for the samples not clustering?

I'm performing RNA-seq analysis. I have used Hisat2 for aligning reads to the genome and stringtie for quantification and extracted read count information directly from the files generated by ...
3
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1answer
992 views

Strange per sequence GC content results

I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination ...
6
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2answers
2k views

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 ...
4
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1answer
96 views

Why is ribosomal RNA difficult to remove even with Poly(A) selection?

In this answer (actually in a comment), it is stated that: As you've noticed from your own analysis, the ribosomal genes have quite variable expression across cells. They're expressed everywhere, ...
1
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1answer
138 views

Optimal design for an RNA-seq experiment with ERCC RNA Spike-In Control Mixes

I am planning an experiment on gene expression. I have 6 conditions and 3 replicates in each condition. I would like to use ERCC spike-in mixes for quality check: lower limit of detection, dynamic ...
1
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1answer
329 views

Alignment QC differences between HISAT2 and Qualimap

I used hisat2 for aligning reads to to the genome. I have an alignment summary for sample1 as follows: ...
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0answers
38 views

NPDock - service unavailable [closed]

NPDock service http://genesilico.pl/NPDock/ is unavailable, at least that's the message that shows after you try to submit a job. It's been like this for the last few weeks. Contact email address ...
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2answers
2k views

How to filter ribosomal RNA from scRNA-seq data

I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA? The only solution I found is SortMeRNA, however it works with raw sequencing ...