Newest Questions
6,612 questions
4
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12
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Duplicate regions in sample cnvkit
I am trying to run cnvkit in the following steps, for context I have tumor only samples from WES dataset:
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2
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answers
8
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Looking for suggestions on tRNA 2D structure visualization tools (MacOS)
I’ve successfully obtained the tRNA molecule data in dot-bracket format, and I’m looking for tools that can help visualize their 2D structures.
Could anyone recommend reliable software or online tools ...
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1
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18
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Looking for a tool to identify all transmembrane proteins in a proteome
I am looking for a tool that identifies all the proteins of a given proteome that are predicted to have at least one transmembrane region. My proteome of interest is available in UniProt, NCBI, ...
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0
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14
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Discrepancies in Docking pose visualization
I’m analyzing the results of a molecular docking study performed with TomoDock, which uses AutoDock Vina.
For the ligand–protein interaction analysis, I’ve been using PyMOL, Discovery Studio ...
0
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0
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8
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Discovery Studio 2D Map Problem [closed]
!I'm not sure why when I look at my bicyclic peptide in the 2D map diagram it looks so strange. Is this a problem with how I uploaded it or from the docking? For docking I obtained Smiles from my ...
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1
vote
1
answer
10
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Normalisation of GEO miRNA microarray data
I am working on a project with 2 datasets, GSE139031 and GSE112264, which are microRNA microarray datasets. I downloaded and ran the data processing from SOFT files to obtain expression data. In this ...
2
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0
answers
6
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Mapping specific Gene Ontology terms to broader PANTHER pie chart categories
I'm working with the PANTHER DB API to analyze gene functions and want to categorize specific molecular functions into broader PANTHER pie chart categories for visualization.
What I've done:
Used ...
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0
votes
2
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19
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Finding all fasta sequences that are one mutation away from a reference sequence
I have a set of roughly 1000 sequences. I've chosen one of these sequences to be a reference sequence, and I want to find all the sequences that are one change away from it (one substitution, one ...
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2
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0
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5
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Error "no rows to aggregate" using makeFunctionalPrediction() Tax4fun2 (R)
’m running Tax4Fun2 (v1.1.5) on Ubuntu via WSL2. The runRefBlast() step completed successfully, but when I call makeFunctionalPrediction(), I get the following error:
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1
vote
1
answer
13
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Cytoscape annotation color cannot change
I am trying to build network clusters in cytoscape from GSEA data and facing two problems. First when I apply filter, it goes back to original if I change between enrichment maps and the filter is not ...
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2
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0
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13
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Mixed 16S/ITS kit but reads look overwhelmingly V3–V4 — how to verify and subset per region?
I am new to metagenomics bioinformatic analysis, as I'm willing to study soil samples microbial diversity. I have paired-end FASTQs sequenced with a kit that can target three regions (16S V3–V4, 16S ...
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I annotated a genome, and the program labeled UTRs as sequence segments/exons. How can I fix this issue?
I used EviAnn to annotate a genome using protein, cDNA, and RNA-data, and it labeled UTRs as as sequence segments/exons before and after the coding region (CDS). Gemini gave me this code to fix it:
<...
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1
vote
0
answers
18
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Numbat to infer CNV: Official hg38 reference files have no SNP overlap, Eagle phasing fails
Downloaded both files last month (Sept 2024) following official tutorial:
...
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3
votes
0
answers
34
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Pseudogene - scarce info [closed]
TLDR: I'm trying to find info on a pseudogene (RNA5SP352) and simply can't. Any help or indications would be greatly appreciated.
So, I'm currently studying a master's degree related to Biology, and ...
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1
vote
1
answer
25
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How much coverage is needed for high-quality phylogenetic and admixture analyses using short-read WGS in plants?
I’m planning to do short-read whole genome sequencing (WGS) and genome assembly on my plants. How much coverage do I need to get reliable results for phylogenetic and admixture analyses?
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