Newest Questions
6,549 questions
1
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32
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STACKS process_radtags for demultiplexing RAD-seq data returning 57.5% "barcode not found" drops, retaining only 41.2% of reads
I'm having a very specific issue with demultiplexing my single-digest RAD-seq data using STACKS process_radtags. I have 389 individuals across 5 different libraries,...
- 11
1
vote
0
answers
5
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BioID SAINT downstream analysis
I have SAINT results which contain 2 types of baits CCER2-C and CCER2-N. I need to determine proteins which interact with CCER2-C vs CCER2-N. I have come across heat maps and dot plots by Prohits-viz ...
- 153
0
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0
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8
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ChimeraX AlphaFold3 prediction pseudobond naming
I had a question about how to label the residues between which pseudobonds occur in ChimeraX 1.9.
I generated pseudobonds by using the PAE output from AlphaFold3 and the command
...
- 1
0
votes
0
answers
28
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Choosing between Intel and AMD for bioinformatics and molecular dynamics workflows on Linux
I’m in the process of building a workstation for scientific computing, primarily focused on bioinformatics and molecular dynamics simulations. My daily tasks include:
• Genome assembly and ...
1
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0
answers
11
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Anomalies while docking and visualising using Python on Colab
I need some help with what I am trying to make. This program/tool aims to perform the entire molecular docking and visualisation process on a Jupyter Notebook in Colab, without having to manually do ...
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1
vote
0
answers
10
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GRaNIE package: the output contains the wrong rat genome assembly
I initialize the gene regulatory network with the appropriate genome assembly and ensembl version for my data:
...
- 11
0
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0
answers
11
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Association (Protein interaction) in Intact database results what can really mean?
I'm looking for every possible interaction between proteins. Many results were association (not physical just "association"). The interaction detection method were anti tag ...
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0
answers
20
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Warning in bcftools when subsetting a VCF by variant ID
I have successfully subset a VCF by variant ID after phasing and imputing using Beagle 5.5, however, I am getting the warning "[W::vcf_parse_info] INFO 'END' is not defined in the header, ...
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3
votes
1
answer
15
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Getting organism information from the ENA API
I have been generating Snakemake sample tables from a GEO identifier (GSExxxxxx) directly by making requests to the NCBI and ENA APIs. It works, but with some caveats (explained in this open question: ...
- 767
0
votes
1
answer
19
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Combining SCTransform, FindIntegrationAnchors, and Harmony
I'm trying to integrate 9 scRNA datasets from different publications. When using SCTranform combined with IntegrateData using anchors, the resulting UMAP is fairly noisy with some clear batch effect. ...
1
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1
answer
12
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Installation of biogrid2 plugin in cytoscape
I'm trying to install the Biogrid2 plugin in the latest version of cytoscape (v3.10.3), but I get this error:
...
- 11
3
votes
1
answer
31
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Construction of 1000 genome phase 3 reference panel
Currently I'm learning to merge reference panel with WGS data to attain a more population-specific panel for imputation of SNP array data.
But I face 1 issue, it is not clear how to construct ...
- 31
1
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0
answers
7
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Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under the same condition
I am working on translation efficiency analysis in Nicotiana benthamiana. To do this properly, I need paired RNA-seq and Ribo-seq datasets collected under the same biological condition (same tissue, ...
-1
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0
answers
19
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How to respond the comment on the sample size in qPCR
In my bioinformatics article, I discuss the identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis prognosis. In the experimental stage, Tissue samples from three case ...
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1
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0
answers
14
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Unable to install cytoscape on the new version of sequoia (15.4.1)
I get this error message when trying to open the installer:
You can’t open the application “Cytoscape Installer” because this application is not supported on this Mac.
I am pretty sure this is ...
- 11
2
votes
1
answer
19
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What tool to use for visualizing combined TF binding sites and H3K27me3 enrichment across multiple cell lines using deepTools?
I'm analyzing ChIP-seq data for the transcription factor of interest (TF) and the H3K27me3 histone modification across three different cell lines: H9, HSMM, and iPSC. For each cell line, I have:
TF ...
1
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0
answers
36
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CRISPR Screen Alignments Mystery
I am analyzing a CRISPR screen. Illumina MiSeq, 5 million 75PE reads, and a PhiX spike in of 10%. The experiment is a depletion CRISPR library over time of a cell line.
It is a subset of 700 guide ...
1
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2
answers
18
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Will Cytoscape allow me to draw a network piece by piece and test claimed interactions?
As a scientific editor, I sometimes need to envisage proposed gene–enzyme–metabolite networks while editing papers. Being a visual thinker, I have to plot the claimed interactions and effects (as ...
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2
votes
0
answers
25
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What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
I was looking into the JASPAR database for transcription factor binding motifs related to Neurod2, and I found two ids:
MA0668.3
MA1993.2
Both IDs correspond to the same transcription factor (...
- 21
4
votes
0
answers
43
views
Understanding NCBI eutils API results
I have made a Python function that can turn an NCBI GEO identifier (GSExxxxxx) into an ENA bioproject accession using the NCBI API. I need this to get sample tables which I then feed into Snakemake. ...
- 767
0
votes
0
answers
20
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Cytoscape stringapp takes too much time getting protein queries and cloudflare's servers time out
I'm trying to load a list of 19153 genes in Cytoscape with the stringapp protein query, but since the list is gigantic, it takes a lot of time to gather all the protein names and cloudflare's server ...
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1
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0
answers
12
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Automated Molecular Docking Script for Library of Receptor Proteins and Singular Ligand
My experiment is to see if a lipid molecule binds to the surface proteins of a class of cells, to see if there is potentially an interaction.
I am relatively new to molecular docking, but am curious ...
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0
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0
answers
9
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Inquiry about using EMBOSS MATCHER with Python
I am new to Bioinformatics and want to know if this is possible. I have a .txt file with a series of 50 gene sequences and I want to know if I can find the identity of them iteratively through a ...
1
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0
answers
45
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Add statistical test to this ggplot boxplot in R
Good morning,
I was wondering if anyone could assist me with the following: I am struggling to add a statistical test to this boxplot like a bar (preferably with Wilcox test). I tried with adding ...
- 65
1
vote
1
answer
126
views
How to subset a large BAM file using BED file?
I have few NIST BAM files which require to be filtered for reads that are overlapping regions with the BED file. I have tried the following command using samtools:
...
2
votes
1
answer
23
views
Weighted mean allele frequency (x-chromosome) calculation
This is a well-known formula that I found in a printed book:
$AF = \frac{(AF_{female} \hspace{4mm} \times 2 \times N_{females} \hspace{4mm})~+~(AF_{male} \hspace{4mm} \times N_{males} \hspace{4mm})}{2 ...
- 131
2
votes
0
answers
12
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BEAST Low Posterior ESS and Posterior Support Values for MCC nodes
I've been working with BEAST for the past couple weeks to try to make a comprehensive phylogeny of 16S for a genus of frogs. There are two groups of interest to me: the mainland clade and the ...
2
votes
1
answer
8
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PSIMI 25 style has disappeared from Style menu in Cytoscape [Cytoscape]
I have used the PSIMI 25 style, which was a built-in style, to be able to easily distinguish human proteins/nodes from non-human ones in Cytoscape (I'm using 3.10.3) networks. This seems to have ...
3
votes
1
answer
37
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analysis of a few genes in RNA-Seq datasets
I'm analyzing the gene expression of three genes in several RNA-Seq datasets (each dataset investigates a different disease - I'm evaluating the difference of RNA counts in healthy vs disease).
I'm ...
- 119
2
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0
answers
16
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How to match output alleles of modkit and sniffles2 outputs in the wf human variation pipeline?
I am using the wf-human-variation pipeline to obtain (1) DNA methylation data and (2) structural variation data. According to their documentation, the methylation results are labelled according to ...
- 21
1
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0
answers
57
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Getting fragments inside window using pysam
First of all, I'm new in processing bam files with pysam so sorry if this is a very basic request.
I want to extract fragment lengths mapping to genomic regions of interest and then get some custom ...
- 11
2
votes
0
answers
20
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Mutect2 analysis mode
Can we run a tumor-tumor analysis with Mutect2, like we do tumor-normal?Where in the tumor-tumor mode, the samples are treated and untreated tumor samples?
My goal is to identify two scenarios in my ...
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1
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0
answers
22
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How to visualize correlation between two ChIP-seq profiles (e.g., protein X and H3K27me3)?
I have ChIP-seq data for two factors: protein X and H3K27me3. If I generate separate heatmaps or coverage tracks for each one, I understand that this will only show their individual distributions ...
4
votes
2
answers
47
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Legends with ggplot
I am trying to generate a plot with mean and standard deviation but I am having some difficulty with the legend.
As you can see from the image, the legend title "Statistics" appears two ...
0
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1
answer
29
views
Snakemake: WorkflowError: Target rules may not contain wildcards
I have this very simple Snakefile, I trimmed it down to a minimum:
...
- 767
0
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0
answers
12
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Single cell long read transcriptomics
I am analysing single-cell long-read RNA-sequencing data that I got from ONT. The aim is to look at differential isoforms in the condition vs control in different cell types. I started with QC of the ...
2
votes
0
answers
28
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Unexpected sequences extracted from BLAST database
I have downloaded the BLAST formatted nt database from https://ftp.ncbi.nlm.nih.gov/blast/db/ and I'm trying to extract sequences using an accession number list obtained with esearch and efetch. ...
- 21
0
votes
1
answer
30
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Different layout after saving Cytoscape network
I am new to Cytoscape and thus I use for now the application. I am working on a network of nodes trying to observe changes in clusters and distances from nodes over time.
In brief, I want to make a ...
0
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0
answers
14
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Fscore in BBrowserX
I'm using BBrowserX for pathway enrichment analysis and have come across the F-score in the results. Could someone explain how this F-score is calculated within BBrowserX. Thanks!!!
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1
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0
answers
20
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Sequence-Based Ligand Binding Site Prediction Tools (Alternative to PrankWeb with PDB Input)
I'm doing it for the Davis and KIBA datasets so that's around 660 sequences
Are there any tools or web servers that predict ligand binding sites from protein sequences alone (without requiring a PDB ...
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2
votes
1
answer
80
views
Nextflow channel value to string conversion
A process outputs a string that is generated in a bash command as either env(myVar) or as a stdout:
...
- 659
1
vote
1
answer
44
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Fastq mapping to different genomes in Geneious
I sent a sample containing 3 different bacteria for WGS. I received fastq files. I want to map these files to the bacterial genomes to determine the proportion of different bacteria in the sample. I ...
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0
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0
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31
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How to efficiently rank the genes in a transcriptome dataset by signal2noise ratio?
GSEA by broad institute is really a powerful tool to handle this analysis very efficiently compared to other packages such as clusterProfiler. Specially it comes with the MsigDB curated genesets for 3 ...
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0
answers
8
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How to analyse intersections and differences between stripped region-specific VCF files generated from SURVIVOR + AnnotSV?
I'm trying to identify intersections and differences in the occurrence of structural variants (SV) between different regions of Africa (N Africa, W Africa, C Africa, E Africa, S Africa). The files I ...
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0
answers
21
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Why is Biotite not returning correct hbonds count?
According to HBPLUS, 5i55.pdb has 44 hydrogen bonds.
...
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3
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1
answer
70
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How can I group mitochondrial heteroplasmy into bins based on age
I have mitochondrial heteroplasmy data obtained from ddPCR that I am trying to group into age bins. One bin edge has to be 0. I would like to dynamically choose all the other bin edges.
Each bin ...
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1
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0
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35
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Hard Filtering Differences between WES and WGS
I am working on human WGS data and i need to detect SNPs and INDELs, during the variant calling step i have to use a filter to remove false SNPs or in general bad quality SNPs, i am wondering if I ...
1
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1
answer
59
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How can I visualize read depth from sequencing data?
This question was also asked on Biostars
I am currently on a genomic variants analysis and have completed the alignment step (BQSR and Apply , depth sequencing....). If any of you can help me or ...
1
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1
answer
40
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Install DCA and its dependencies
I am trying to install DCA but it fails due to dependency issues. The package is no longer being maintained. Following are the commands I need to run:
...
- 153
2
votes
1
answer
23
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Reference genome masking reason for particular position
I'm trying to use an alignment tool like BLAST (in fast LAST) with the hg19 masked genome, but it is failing to find a sequence at a particular location, and I've determined that it is due to the ...
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