Questions tagged [rna-seq]
Questions should include this tag if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design or transcriptome assembly...
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Should I include unannotated transcripts in a pathway enrichment analysis of a de-novo assembled transcriptome?
I'm trying to perform an enrichment analysis on a set of Transcripts assembled de-novo, using a GSEA like method on KEGG and GO. The set contains annotated and unannotated transcripts. My question is:
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Why is RNASpades giving three FASTA output files instead of only one?
I'm running RNASpades for de-novo transcriptome assembly in the Galaxy workflow manager
. Instead of giving only one output of ...
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I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its ...
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RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values
Cross-posted on biostars
Does anyone know where I can find RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values?
The dataset must contain genotypes and annotated .
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Figuring out operons from prokaryotic RNA-Seq data
I am looking at a couple of unpaired prokaryotic RNA-Seq datasets. These data have been obtained from bacteria (cultures likely axenic, not guaranteed). My aim is to figure out whether my genes of ...
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Protein atlas rna-seq vs protein expression region missmatch
I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in ...
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PCA of bulk RNA-seq doesn't show clustering and show large variation in general
I am very new to analyzing RNAseq and I am in a group with very little experience in this regard and I am looking for some advice.
My PCA after performing DESEQ2 analysis on my dataset doesn't show ...
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How much should the 5' adapter and i7 sequence differ?
In a multiome (RNA and ATAC) project I'm working on we chanced upon a strange situation. We're not sure if it poses a problem or not and would like to know if and where I can look it up if necessary.
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Reasons for extremely low number of DESeq identified differentially expressed genes after RNAseq?
I am fairly new at RNA-sequencing analysis, but I have attempted to analyse the data I obtained from RNA sequencing on my own by following an online EdX class and by basing the majority of the ...
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RNA-seq QC and alignment error in script
I am analyzing bulk RNA-seq data for Paired-End. I have separate scripts for fastqc, STAR & qualimap but want to run them in a single script which looks like this
USAGE: sh rna-qc.sh <path/to/...
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time*treatment series with repeated (i.e: NOT independent) sampling of replicates
I am performing the analysis of cell cultures in suspension, untreated(U) and treatment A and B, at t0, t1 and t2, 4 replicates per treatment.
The experiment started with 12 cultures, 4U, 4A and 4B, ...
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Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
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Find most abundant transcript isoform of a gene across different tissues in long read RNA-Seq data
I want to understand which is the most abundant variant of a gene of interest across different tissues by looking at different publicly available databases (mouse/human). I have deduced from ...
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Predicting gene expression, RNA-seq, from regulatory signals, ChIP-seq
For a given cell line, I have ChIP-seq and RNA-seq data. I am trying to construct a model for predicting gene expression from ChIP-seq. Basic models I have seen [a very simple model is described in ...
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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 ...
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