Newest Questions
6,549 questions
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How to view the position of certain sequence in IGV?
I want to know where a certain sequence occurs in my genome in IGV. I searched by "Tools --> Find Motif". Two new tracks appeared ("<sequence>" and " Negative"), ...
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1
answer
61
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medaka_variant does not work, but medaka variant command does
I've installed medaka via conda without difficulty. However, I don't seem to be able to get the typical command medaka_variant to work. However, ...
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3
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0
answers
34
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Sankey plot for unequal node sizes
I am trying to plot a host-parasite-pathogen network using a sankey graph and I am having problems scaling the nodes to their occurrence (counts). The main issue is that the
host count is nested in ...
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2
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2
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19
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add legend of clusters after MCL cluster network analysis
I have installed String app on Cytoscape and imported a list of protein of interest. I run the cluster network (MCL) analysis to visualise my network in different clusters. I now have all the proteins ...
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1
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1
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49
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NGS Data analysis: Filtering Raw reads and Removing adapter sequences
I have NGS data of 8 different samples of human brain RNA sequences (Novogene). Each sample has 2 .fq.gz files.
I plan to filter the raw reads, then align the ...
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2
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2
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61
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Why my samplelist.csv table for nf-core/chipseq workflow is not working?
I’m new to the nf-core/chipseq workflow and I’m currently stuck on preparing the samplesheet.csv file. I’m trying to set up the ...
1
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1
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29
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How can obtain a significant expressed genes list when we have only two sample? (one sample per condition)
I am doing a Bulk RNA seq analysis with one sample per condition.
I have problem with the "Identifying significant Differentially Expressed Genes (DEGs)" part. This is the Volcano plot that ...
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2
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0
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Precise Mathematical Expression for Replication Fork Numbers in the Cooper-Helmstetter Model of E. coli
I am researching the Cooper-Helmstetter model of DNA replication in E. coli, specifically focusing on the mathematical expression for the number of replication forks ($F_i$). After understanding the ...
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1
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Problem with gaps and coverage in haploid assembly
This question was also asked on github
I am using Canu to assemble a yeast haploid genome from PacBio long reads, and I have encountered an issue related to the use of purge haplotigs.
After running ...
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1
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10
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Arriba inferring type deletion in fusion detection
This question was also asked on github
I am inspecting the ARRIBA documentation and I am confused on the type field they provide in the ...
- 151
1
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0
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22
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Small pVCF file along with some phenotype information for RVAS tool testing
I'm developing a pipeline for RVAS (Rare Variant Association Study) where variants are aggregated on the gene level before doing some Burden or SKAT tests. I need a small, publicly available or ...
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1
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0
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13
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Runnning Protein model processed in CHARMM-GUI in GROMACS 2025.0. Getting errors about Urey-Bradley potential in EM step
I'm a PhD student from a developmental biology background. I'm currently working on simulations using GROMACS 2025.0, running CHARMM27. However, I'm encountering an error related to the Urey-Bradley ...
1
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1
answer
47
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What should be the best strategy to define grid box in blind docking?
I am attempting to perform blind docking using AutoDock Vina , and for being able to form a grid box that covers the entire protein : I find the center coordinates by taking out mean of all the x, y ...
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2
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52
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Variant missing in WES Analysis
I hope you are all doing well. I analyzed the FASTQ files (WES) from a patient with symptoms of deafness on a rented server. I identified the specific variant and reported it.
I no longer want to use ...
3
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1
answer
58
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How is basecaller Phred score quality related to the signal strengh strength (SNR) of a Nanopore sequencer?
I would like to have a very high accuracy Nanopore basecaller program. I know that ML models might train better with noisy data but having a noise-aware program can be useful I think. Ultimately we ...
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