Questions tagged [rna]
Use this tag to refer questions that are related to rna sequence.
89
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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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253
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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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324
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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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3
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332
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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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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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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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2
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64
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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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3
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243
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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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1
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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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3
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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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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 ...
AKV
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answer
30
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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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627
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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
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2
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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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139
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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
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3
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202
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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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4
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1
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379
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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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2
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3
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320
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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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1
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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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3
votes
2
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942
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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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224
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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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430
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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 ...
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5
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2
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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?
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338
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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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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 ...
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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 ...
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2
answers
4k
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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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4
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184
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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, ...
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1
answer
235
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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 ...
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495
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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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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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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 ...
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1
answer
95
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How to compute the chance of failing to detect a gene given the detection limit of a protocol
In Shapiro et al., when discussing about loss of molecules as source of error in single-cell sequencing, it is written that:
Another source of error is losses, which can be severe. The detection ...
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2
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298
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Estimate the length of poly-A tails from randomly-primed RNAseq data
So a poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule.
For my project, I would like ...
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2
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1
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43
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Simple Affy Differential Expression
I think I have a fairly easy-to-solve problem.
I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total.
So I ...
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4
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716
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Basic questions about GSEA
I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, ...
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110
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How can I dock a protein to a nucleic acid?
I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.
What tool can I use?
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What to use to edit RNA alignments?
I have many alignments from Rfam Database, and I would like to edit them.
I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ?
e....
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How to extract RNA sequence and secondary structure restrains from a PDB file
I'm trying to find a programmatic way to automatically extract the following information from a PDB file:
RNA sequence
Secondary structure restraints in bracket format, e.g. ...
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