Questions tagged [transcriptome]
The set of all transcripts of a biological entity, e.g. the transcriptome of a single cell, of a tissue, of an organ, of an individual, of a species. Can also be used to refer to a subset of the transcriptome, e.g. the polyadenylated transcriptome, given that often experiments ignore the 99% of transcripts that are ribosomal RNAs.
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How to only enrich sensible GO and KEGG terms?
I'm thinking of analyzing enriched pathways using KEGG and GO databases on de-novo assembled transcripts using clusterProfiler 4.0. After annotating them with ...
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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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How to identify a bacterium species from its short RNA-seq transcriptomics data?
I am new to RNA-seq analysis and wanted to ask if there is a method to reliably identify the species of a microbial organism using only its raw short RNA transcriptomics data. Here are some of the ...
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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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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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Most-abundant isoform identification using 10x scRNASeq 5' short-reads
I have read a couple of publications related to the question being asked here, and have concluded that quantification of isoforms for scRNASeq experiments is typically coupled with long-read ...
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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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After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
I have been running nf-core in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA ...
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Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
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Low fraction reads in cell metric in snRNA-seq data
For some of our snRNA-seq samples we are finding low fraction of reads detected in single-nuclei rna-seq samples from cellranger, while the other metrics are perfect.
While I understand this could be ...
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Transcript vs Primary transcript on phytozome
Could someone help me understand what the difference between transcript and primary transcript on phytozme is? For example, this dataset of A.thaliana has "primary transcript CDS" vs CDS.
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pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
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How to find specific types of assemblies for specific species using entrez tools?
How to find specific types of assemblies for specific species using entrez tools?
Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.
I can use this ...
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