Newest Questions
6,550 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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1
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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
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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
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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 ...
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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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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:
...
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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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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
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1
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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: ...
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13
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Unix command to copy files with certain ending [closed]
I have a folder, on a Linux system, which has several subfolders and each subfolder has a file which ends with mixed_data.csv (e.g. ...
- 65
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1
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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. ...
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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:
...
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3
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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 ...
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1
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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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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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