Trending questions
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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,...
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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 ...
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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 ...
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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
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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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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:
...
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1
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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: ...
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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. ...
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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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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 ...
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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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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:
...
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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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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 ...
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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 ...
