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ATAC seq density calculation

This paper Fig2b b Changes of chromatin accessibility in AMD (n = 14) relative to normal (n = 11) in all retina samples. Each dot represents one ATAC-Seq peak. Blue line in the left panel indicates ...
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1answer
8 views

Dataset showing evolution of gene

As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
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0answers
6 views

Snakemake fails because it cannot create logs inside a read-only Singularity Container

I am using Snakemake from inside a Singularity container. Because of that, the directory that Snakemake wants to log to cannot be created, and I get an ...
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0answers
24 views

SLURM script for running RSEM star fails

If you have worked on cluster with submitting jobs, please help me in resolving the following error. I am running rsem pipeline to generate star index. In principal STAR requires more than 30G of RAM ...
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1answer
18 views

Does this shape has two clusters or one?

This cluster belongs to the direction of one side group from a long peptide during the simulation. I tried to make each cluster has its own color by those lines, Does that right? ...
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0answers
20 views

How to fix SLURM HPC error regarding topol file . .

first of all I have no idea what I'm doing since all of us in my degree program are stuck with computational undergraduate thesis since we have no face-to-face classes. Our curriculum in BS ...
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0answers
11 views

How to identify specific motif for chip-seq data

For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
3
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1answer
39 views

Create new range based from existing range (python)

I have a pyranges object that I am looking to iterate over. For each range, I would like to "resize" it to its centre (so start+end/2) and save that into ...
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0answers
30 views

Spanning deletion conversion

I have a vcf file created with GATK with spanning deletion https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele- and I now need to compare this VCF ...
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0answers
14 views

going from probe sequence to hgnc gene symbol

I have a bunch of (human) Agilent probes (both probe ID and the actual sequence, some custom array), and I would like to get the hgnc gene symbol based on the actual probe sequences, rather than the ...
1
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1answer
31 views

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
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0answers
19 views

Median string problem & multiple sequence alignment

I read about the median string problem as an introduction to the multiple sequence alignment, however none of the MSA algorithms used seems to be using the idea of finding the median string. To my ...
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0answers
22 views

Convert DNA raw data between a different formats

I have .vcf file with partly decoded genome provided by some service. How can I convert this file into other popular formats which may be used in other services? I'...
1
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1answer
26 views

Upgrading guppy basecaller on Oxford Nanopore Gridion via PPA

I am trying to update the guppy_basecaller (current version installed is 3.2.10+aabd4ec) on a ONT Gridion device. I am initially trying to update it via the ...
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0answers
34 views

Retrieving Co expression data from a Seurat object

I know that this topic has been discussed in other threads, but I never found a definitive answers (and maybe there isn't one) about assessing coexpression in single cell data. I want to assess the ...
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0answers
13 views

About optimal distance (or dissimilarity) measure in proportion data

If we would like to use data with proportion (e.g.,total sum scaling or compositional data), what kinds of distance or dissimilarity can we use? Bray-Curtis is one of them, but does this make sense to ...
0
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1answer
19 views

STRINGdb: reverse map STRING identifiers to gene names?

Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names? For example, the entire STRING network can be downloaded using the ...
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0answers
14 views

Global alignment between two sequence X and Y with maximum number of identical matches

If 2 protein sequence X of length m and Y of length n and if there are several highest scoring global alignments, then I want to get one alignment that has largest number of columns in which a letter ...
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1answer
19 views

Nanopore data clarification regarding merging of samples

We had same set of sample ran on nanopore platform twice. The issue on hand is. First run was done it was nearly done but the power went off. Second run was done completely with enough sequencing ...
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0answers
8 views

How to perform KOG classification?

I have a list of DEGs and I want to perform KOG functional analysis, I try this method but WebMGA is not updated and seems to be deprecated. Are there any other online or standalone tools available ...
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0answers
16 views

What are good resources to learn the basics of graph theory

I just spent half a day "debugging" a script that tried to get the betweenness centrality of a weighted graph with negative weights. However the package I used for that julia's ...
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0answers
20 views

Proper scatter/gather of bam files

I'm trying to do some calculus in parallel with BAM files. For that, I need to split the input bam file in chunks, process them in parallel and join them at the end. But I'm facing a read duplication ...
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3answers
83 views

Filtering Sequences (entries) by headers ID from a Fasta file database

First of all, sorry if this question has been posted previously (I could not found a solution accessing the previous Q&A). I have a fasta file as follow: ...
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1answer
34 views

Explanation for RNA-seq samples not clustering in PCA as expected

A colleague is analysing RNA-seq data - the study design is 2 treatments, 3 replicates, 3 tissues. In their PCA plot the samples clustered neatly by tissue. Except for two samples - two tissue samples ...
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0answers
20 views

How to Interpret Author's Methods in this article?

I have to reproduce a result for school reasons (bioinformatics exam) and I was assigned a certain article. In particular I have to reproduce what some authors did in: doi: 10.1371 / journal.pone....
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0answers
18 views

Reliably create female and male individuals in a -ped file for plink

For a study I need some kind of "decoy" GWAS-data. For this I created a panel with some genes, the same ones as in the real data. From NCBI I fetch some of their SNPs and create my own ...
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1answer
21 views

how to get access to genotypes and phenotypes used for a GWAS

I'm a master's student working on genomic prediction of complex traits using deep learning. i'm looking for a dataset of human genotypes and phenotypes that has been used for a GWAS. The only thing i ...
0
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1answer
11 views

extract chimeric and multimap reads from bam file

I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use htslib for parsing sam/bam files ...
0
votes
1answer
26 views

Making PLINK compatible files from VCF file without phenotype information

I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs ...
0
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1answer
24 views

Differential expression analysis for a subset of transcripts

I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of ...
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0answers
22 views

multi--platform GEO analysis based in expression of single gene

I have a challenge in analyzing GSE34941( It has 4 platforms) according to the expression of a specific gene in R. First, which is the best way to group my patients according to the expression of a ...
0
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1answer
37 views

Do you know any virtual screening libraries with small, soluble compounds?

I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
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0answers
27 views

Not Able to pull genes due to file.fa error

I've recently been pulling TLR genes for different species and keep running across an error called file.fa whenever I start pulling them. Whenever I pull the first gene it's fine and makes the file.fa ...
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1answer
24 views

How to determine a correct promotor sequence? (Bisulfite sequencing - uni assingment)

aspiring bioinformatician here, I'd like to ask you for help with an university assignment. First let me post the entire question: ...
2
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0answers
22 views

Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known TEs and unknown ones. How do we know whether some of these may actually be a functional domain of a gene? It's predicted as repeats may ...
0
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1answer
40 views

co-occuring genes in my list

I have a files which has columns representing genes,sample numbers and sample names (55). The genes are displayed by occurrence in the samples (highest to lowest-55 and 2).I wish to calculate the ...
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0answers
12 views

phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
1
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1answer
50 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
-1
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1answer
74 views

Multiple box plot

I am using below code to plot multiple box plot but I am still struggling to understand how I can add whisker to box plot and how to change sample order like in this figure SampleType? ...
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1answer
23 views

How can I run the latest version of samtools on Slurm?

I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I ...
1
vote
2answers
69 views

Obtaining Whole Genetic Sequence

As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this? ...
0
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0answers
21 views

PDB: Download all biological assemblies

I was wondering if it is possible to download all biological assemblies from the PDB at once (so not the standard asymmetrical files). For example, I want a file containing the coordinates of all ...
2
votes
1answer
20 views

How can I use my Myheritage DNA results file for further analysis?

I had my DNA tested by Myheritage and they sent me a csv file with RSID, Chromosome, position and result (which base) with about 700,000 rows. I understand most analyses of DNA use VCF files but is ...
0
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1answer
34 views

How to perform bowtie2 analysis with slurm?

I am trying to run my alignment script that works locally, using SBATCH. Official manual for bowtie2 says I can use ...
0
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0answers
23 views

Ligplot: how to define path in Ubuntu

I installed Ligplot on Ubuntu and have a question. When I open a docking I get the error: Unable to create log file in temporary directory: C:/tmp . I already tried to change the path in several ways ...
0
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0answers
14 views

How to calculate dN/dS for all ortholog group? [closed]

I have managed to generate json file for all ortholog groups (4000) under HyPhy using BUSTED, SLAC and FEL. From the output, how can i find the dN/dS and how shall i compare among all of the groups ? ...
0
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1answer
61 views

Supplementary aligments in VAF

I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot. I'm interested in what is done generally, if there is a "rule" ...
0
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0answers
21 views

How to read E-value annotation on NCBI BLAST?

i am a bit confused how to read the current E value annotation on NCBI BLAST results. I looked into the matter but could not find an factual answer . What i understood so far: E -values are the ...
1
vote
1answer
56 views

Are there open-sourced graph-based variant callers?

I would like to compare GATK with graph-based variant callers. I have seen the Fast and accurate genomic analyses using genome graphs paper from SevenBridges and the paragraph tool by Illumina though ...
0
votes
1answer
16 views

Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...

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