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Drug indication data for only cancer phenotype from Chembl

I am interested in getting the drug indication data for all drugs in the database using sqlite. I used following step to get this ...
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  • 117
1 vote
0 answers
14 views

How can you put a bash array into a wdl variable?

Given two separate wdl arrays, my command section will do some modifications to each array and place the output into two separate bash arrays. Finally, I want to output the two separate bash arrays in ...
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1 vote
0 answers
18 views

How to use EPAM Cloud Pipelines?

I am searching for an easy-to-use GUI management tool to handle my WDL workflows, I found EPAM Cloud Pipelines. Unfortunately, it uses cloud services such as AWS, GCP, etc. but I wanted to use my own ...
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0 votes
0 answers
9 views

Looking for FET-PET brain dataset

I have searched the internet for a public dataset containing human (FET-)PET brain images. This could be healthy brains OR glioma/glioblastoma brains. As far as I can tell, this does not exist? All ...
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0 votes
1 answer
13 views

how to create "sample file" for the qAlign() function after trimming the reads in R

I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?" I did trim the ...
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1 vote
1 answer
23 views

What is the best way to perform batch ajustment between two experiments?

I have duplicate drug efficacy experiments performed six months apart. I would like to know what is the right way to perform statistical analysis to understand fold changes after treatment with a drug....
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  • 11
1 vote
1 answer
19 views

Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
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0 votes
0 answers
4 views

IsoPlexis Data Analysis

Has anyone analyzed the raw data output from IsoPlexis secretome profiling? I want to make use of this data outside of their "end-to-end" software.
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-3 votes
0 answers
26 views

How to convert a WDL file to a JSON file? [closed]

I want to convert a WDL file into a JSON using python.
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1 vote
1 answer
38 views

Violin plots appear as vertical lines

I want to perform a violin plot from a Seurat object and I rather have vertical lines. How can I stop this and rather have a standard Violin plot? code ...
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  • 487
1 vote
0 answers
15 views

chip seq biological replicate merge after peak-calling

I have 3 biological replicates for KO condition. What I have done so far Peak calling The removed blacklisted region Now Im bit confused about the peak merging stage. Here Im trying to use the ...
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  • 1,538
1 vote
0 answers
9 views

What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?

I am interested in the differences between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus. They yield the same results as seen in the code below. ...
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  • 153
0 votes
0 answers
20 views

Extract SNPs from multiple sequence alignment

I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
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  • 1
0 votes
1 answer
12 views

Where to download a table with ICD-9-CM codes?

I am looking for a simple table with all ICD9 codes (For example: Diagnosis Code 414.0 -> Coronary atherosclerosis). I can only find weird PDF or other kinds of text documents. Or web forms, where ...
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  • 1,181
3 votes
1 answer
62 views

What does this accession NCBI code mean: 6MWN_B?

According to this article, accession codes should consist from a combination of uppercase letters following a combination of digits. If this is a RefSeq, it can have a prefix as a combination of ...
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  • 305
1 vote
0 answers
20 views

Cytoscape for coloring the nodes in the network

I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R? My input is 2 column ...
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0 votes
0 answers
9 views

How to access BOLD timeseries data using atlas-Schaefer2018_desc-400Parcels with Python?

So basically I have this code ...
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  • 1
1 vote
1 answer
36 views

How to build advanced boxplots from datasets which columns contain only numbers?

I have got a fold-change dataset and I simply would like to plot something like this: The problem is that I have only numbers in my columns and when I use a boxplot() function I can plot only boxes ...
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  • 101
0 votes
1 answer
49 views

Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?

As we know, the amount of RNA reads per cell obtained from 10X scRNA experiment vary between cells. I wonder if this is effect of technical issues or does the number of RNA reads per cell obtained ...
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1 vote
0 answers
11 views

Cromwell - controlling core/mem usage, and CallCaching, while running locally?

I'm sitting on a mountain of microarray (.idat files) data, and have been tasked to analyze it. I chose the MoChA pipeline, developed by the Broad Institute. It runs through Cromwell, of which I know ...
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  • 11
1 vote
0 answers
8 views

Creating msk file for Illumina Array Analysis CLI Copy number train

recently I'm researching on how to detect CNV from Illumina microarray data. I found that Illumina has Array Analysis CLI software for this task, and I need to train the CN model myself, since the ...
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2 votes
0 answers
41 views

How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline

I have several hundred scRNA-seq count matrices, each from a different sample. For my other dataset containg a few dozen samples, I simply merged everything together into one Seurat object, but that ...
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0 votes
2 answers
27 views

"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)

This question was also asked on github I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
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  • 191
1 vote
1 answer
49 views

ATAC peak anatations

I am new in ATAC analysis. I have a problem about how to transfer ATAC peak to gene symbol. Here is the ATAC-seq: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3271041 The ...
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1 vote
1 answer
19 views

Phylogenetic tree building from proGenomes database for shotgun metagenomics

For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance. I’m ...
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  • 41
0 votes
1 answer
37 views

How to configure Cromwell to work with slurm?

I have a cluster that is set up with slurm and I seek to use Cromwell to dispatch jobs to the slurm scheduler. I followed the description explained on Cromwells Documentation Website. And created a ...
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3 votes
1 answer
32 views

Phylogenetic tree rooting in shotgun metagenomics

But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
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  • 41
0 votes
0 answers
21 views

Krakenuniq mmap error

I built Krakenuniq on an HPC, and I've been trying to run it on my data using the following command: krakenuniq --db DBDIR --threads 1 All_reads.fastq This ...
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0 votes
0 answers
26 views

What genes are driving a certain pathway

I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway. ...
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  • 317
0 votes
1 answer
17 views

Extract chromosome arms' coordinates for specific reference

I would like to get chromosome arms' coordinates for genome reference hs37d5 (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
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  • 1,713
2 votes
1 answer
35 views

What is the difference between Normalized Expression in EdgeR vs DESeq2?

I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why? How to get normalized expression using edgeR: ...
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  • 153
0 votes
0 answers
10 views

For the PLINK --score function: Is there a mechanism to score X-linked SNPs with proper dosage (0, 1 for males; and 0, 1, 2 for females)?

GCTA can produce BLUP estimates (for SNP effects) which are easily lifted over to PLINK via --score on independent samples. GCTA can also perform dosage ...
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0 votes
0 answers
7 views

How to have in home alphafold predicted structure pdbs converted to mmCIF files in line with alphafold standards?

I am using AlphaFold to predict some protein structures of interest, not covered in their DB yet. What I am obtaining are PDB files with atom coordinates like in the line below with no further ...
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0 votes
1 answer
11 views

Repeating indexes of atoms in PDB file

I have a PDB file in which the indexes of atoms are repeated (or better say refreshed) every 99999. I am using MDtraj software to analyze this pdf file, so these repeating indexes cause some problems. ...
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  • 1
0 votes
0 answers
7 views

Comparing loci across catalogs

Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of a plant species, and have aligned my paired-end RAD reads to a reference genome (using GSNAP). The goal ...
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0 votes
0 answers
14 views

Pymol: select low confidence regions from AlphaFold pdb file

I have downloaded a predicted structure from AlphaFold as a pdb file (https://alphafold.com/entry/O75376) and loaded it into Pymol (2.3.0). There is quite a large portion of the structure that was ...
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0 votes
0 answers
10 views

Interpreting 'samtools mpileup' output for multiple inputs

I would like to calculate sequencing coverage for a WGS project. Both long and short reads. I've used samtools as following: ...
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  • 539
0 votes
1 answer
36 views

Pipeline for paired end RNA sequence data to proteins

Forgive the basic question here, but I'm super novice at this ... I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and ...
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  • 101
2 votes
1 answer
24 views

baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
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3 votes
1 answer
51 views

Imputing small region of the genome

If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' ...
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0 votes
1 answer
32 views

Select synonymous sites from a multiple sequence alignment

Could someone kindly recommend a tool or R package that can identify synonymous sites in a multiple sequence alignment? I wish to select those taxa for tree reconstruction and other downstream ...
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  • 1
0 votes
0 answers
14 views

locating hydrocarbon in PDB file

Does everyone know how can I understand whether my PDB file has a Hydrocarbon or not? and how to locate it using VMD
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  • 1
2 votes
1 answer
40 views

scRNA-Seq pseudobulk for marker detection

A standard approach for scRNA-Seq is to partition the single cells into individual clusters, then use a Wilcoxon test to find markers that characterize each cluster (or other statistical methods that ...
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  • 190
1 vote
1 answer
36 views

Error in DESeq2 analysis with dimnames

I'm getting the following error in a DESeq2 analysis and I can't seem to figure out the issue: ...
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  • 153
2 votes
0 answers
16 views

How to retrieve Expression Atlas baseline expression results in JSON format?

I'm looking to retrieve Expression Atlas baseline expression results in JSON format, e.g. the results on this page. Several years ago I did a similar thing but looking at differential expression ...
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  • 51
2 votes
2 answers
45 views

Is the Bowtie2 MAPQ score dependent on the database index?

I have two very similar genomes in my bowtie2 database (nuc similarity > 90 %). When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a ...
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  • 23
0 votes
0 answers
22 views

Can I use a benchmark to choose a clustering or module detection method for a gene dataset?

The paper A comprehensive evaluation of module detection methods for gene expression data says that: "We first want to provide an overview of the characteristics and performance of current module ...
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  • 101
0 votes
1 answer
34 views

Why must a maximal non-branching path be a contig?

The following is from Bioinformatics Algorithms: Fortunately, we can derive contigs from the de Bruijn graph. A path in a graph is called non-branching if in(v) = out(v) = 1 for each intermediate ...
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  • 127
0 votes
1 answer
28 views

Protein-Ligand in PDB

I am a newbie in bioinformatics. In PDB, while searching for proteins, I sometimes get protein with ligand, such as PDB ID 1J1Z. In cases I get pure protein structure, in some cases I get protein-with ...
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2 votes
1 answer
54 views

Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, "nexus"), my kernel got ...
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  • 305

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