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2 views

How to dock multiple ligands

How can I dock multiple ligands (around 20,000) with a protein simultaneously. I went through the online tutorials on youtube but nothing really helped.
0
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0answers
2 views

How to infer if the gene is differentially methylated given the beta values at probe level?

I have identified a set of differentially expressed genes between tumor and normal samples. I want to explore the methylation status of these genes and see if they are differentially menthylated as ...
0
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0answers
4 views

Select for a specific proportion of a genomic feature

Currently have a bed file with exon coordinates for a list of about 20 genes, and I want to select the exons that fall within the first 3/4 or 2/3 of the coding region for each gene. Does anyone know ...
0
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1answer
10 views

Programmatically retrieve Accession List from NCBI

I would like to programmatically retrieve the file "Accession List" from an NCBI page. I'm running firefox, so I'm clicking the file and clicking Ctrl + <...
0
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0answers
6 views

gene set enrichment in single-cell data

Gene set or pathway analysis in scRNA-seq data has its own challenges. Since the data is sparse and many genes will be missing for any given cell, some people simply add up all the counts across the ...
0
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1answer
12 views

Selecting part of an extracted ligand

I have the PDB 6LU7. I extracted the ligand using extract lig, org and then the protein using extract prot, poly. The ligand has three parts: 02J, PJE, and 010. I want to select the 02J and 010 ...
0
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0answers
21 views

comparing two groups using R bar graph

I have two data frames. Let say TissueA and TissueB. I want to compare these two data frames by bar graph in R. ...
0
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0answers
21 views

How do I get repeating regions from fasta file or directly from internet

If I go to ncbi site, apply customize view -> Customize -> All features -> Update view and then ctrl + f : Alu I can ...
0
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0answers
16 views

Trying to retrieve sra data using sra explorer

I am trying to use the SRA explorer tool to download data from ENA. Whatever geo accession number I give it however, it will return no results. It only seems to return results for the suggestions it ...
0
votes
1answer
14 views

RNA seq .counts.txt to bigwig conversion

I've downloaded neuronal RNA seq data from GEO. The files are in .counts.txt format. Could I convert them to bigwig? If so, how?
1
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0answers
37 views

Question about Using MDAPackmol (packmol in python)

I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an ...
0
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0answers
10 views

Identifying substrates with enriched degradation potential from count data of enzymes able to degrade that substrate across all samples

How would I identify if I have enriched degradation of a certain substrate within a clade of bacteria with count data of enzyme capable of degrading a range of substrates? I have started of by ...
0
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0answers
20 views

Non-finite value supplied by optim in Hurdle model of enzyme count data

I have a dataset of enzymes counts that are grouped by substrate they degrade and am attempting to model if the origin of the genome in which the enzymes were found can predict the count for ...
0
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0answers
24 views

Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
0
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2answers
39 views

Python: How to write duplicate sequences removed from fasta file to new file

I currently am using this code to remove duplicate sequences from the fasta file. However, I would also like to write a new file with only the removed duplicates as well as a count for how many times ...
0
votes
0answers
21 views

about the Bray-Curtis distance using 16S rRNA

If we want to calculate Bray-Curtis distance using 16S rRNA, is it better to use normalize counts using DESseq2 and calculate the proportion (normalized counts by total library size) or is it better ...
0
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0answers
21 views

Comparing aligned amino acids to codon

I have a set of 4 amino acids which i have aligned,but i want to compare then with respective nucleotide sequence in terms of change codon level. I have the alignment file where i want to take only ...
1
vote
1answer
18 views

Comparing gene abundances between metagenomes

My workflow until now: Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest Right now I have a ...
2
votes
3answers
304 views

How to reduce the occupied RAM when you are dealing with a very sparse matrix in a single-cell Experiment in R?

I'm dealing with a very large and sparse dataset and the first issues I met occurred when I tried to use quickCluster that reported me this error: ...
-1
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0answers
10 views

Did and why recent studies show superior predictive power using methylation data on early cancer detection?

There seems to be an increasing tend (in both academic and industry) of using methylation pattern for cancer detection / classification. It almost feels that methylation is superior on such task over ...
-2
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1answer
27 views

about the UniProt id and Entrez id

Hi How can we get mapping from UniProt id to Entrez ID? I have UniProt id, but want to convert those ids to Entrez or Ensembl id.
2
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2answers
37 views

how to have a blast xml file in a readable and understandable way

I got a blast xml file after a DNA sequence search. The XML file is not very readable. What is the way to make it more understandable? This blast contains about twenty matches. Here is the xml file
-3
votes
1answer
45 views

Bash script for automatic overlap merging of respective paired-end reads from samples

I have around 300 paired-end files from 150 samples (1 forward and 1 reverse read for each sample). I want to merge (by sequence overlap) respective forward and reverse reads for each of the samples. ...
3
votes
1answer
55 views

Calculating average coverage for .bam files (sequence data)

(Full discolosure that this is my first time working with sequence data, and with the bash scripting.) I need to calculate the average coverage for any .bam file. After some searching I wrote the ...
0
votes
0answers
12 views

ortholog genes visualize in venn diagram

OrthomclToVenn requires a families.txt (this file details which species are in which groups, first the name of the group, then the short handles that appear in ...
0
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0answers
11 views

e-utils api: get chromosome position for each snp on a gene

So I have the following e-utils api-link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json it returns all the SNP-ids for the gene with ...
0
votes
2answers
37 views

What does aov(glm model) actually do in R?

What is happening when you use aov() on a glm model in R? Normal glm model sumamry(m1): ...
0
votes
0answers
8 views

What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?

I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which i view in excel), a 'source Gene ID' is given for each ...
-1
votes
0answers
29 views

How to download taxonomy table from blast ncbi?

After doing a blast analysis, at ncbi's platform, I received the taxonomy table like one showing below. I would like to download this table. There is no command available from the platform. Copy and ...
0
votes
1answer
57 views

Remove Redundant Sequences from FASTA file in Python

I'm attempting to remove redundant sequences from a fasta file (from NCBI). When I execute this code, it returns the number of spots, not the number of sequences. (Number of spots: 408,293, Number of ...
0
votes
1answer
25 views

Is there a way to customize what observations are plotted in ComplexHeatmap?

So right now my observations in the dataset I've processed is stored as sample identifier columns and gene rows: an example of this would be for sample 1 and gene TRIM21 the observation is Missense ...
1
vote
1answer
33 views

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
0
votes
1answer
18 views

classifying samples by TCGA signature

I have some RNA-seq samples from multiple glioblastoma tumours that I'm now trying to classify according to a specific gene signature (from Verhaak et al., 2010) using R. The gene signature is ...
2
votes
0answers
35 views

How to calculate module-trait relationship when trait data is in binary format?

I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
0
votes
1answer
22 views

How do I convert an Excel file (.xlsx) to an .smi file format?

How do I convert an Excel file(.xlsx) to .smi file format? The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
1
vote
2answers
48 views

How to create a list of differentially expressed (DE) genes after normalization with RUVSeq?

I am using edgeR to perform differential expression (DE) analysis on a set of RNA-seq data samples (2 controls; 8 treatments). To correct for batch effects, I am using RUVSeq. I am able to get a list ...
2
votes
2answers
42 views

Error after trimming illumina adapters

I am removing illumina adapters of the NGS data with a loop. My NGS data is storage in /data/HTS_seq/. I used this function: ...
0
votes
1answer
38 views

how to extract a different substring for each row of a dataframe in R?

I have a dataframe with putative alignments of thousands of probe sequences. I would like to pull out the adjacent nucleotide from the genome for each alignment. My dataframe includes ...
0
votes
0answers
26 views

How do I delete ligands from a list of 50,000

I need to delete ligands from a list of over 50,000 ligands in a .sdf file format. Is there any easy and quick way of deleting the ligands from the list. Thank you, Dr. Hussain.
1
vote
1answer
16 views

Do I need to fill in missing side chains and loops before protein-ligand docking for VLS?

I am going to screen a set of small molecules against a CYP450 2C9 protein target. The structure I am using exactly is 5A5I. Do I need to fill in missing side chains and loops before performing VLS? I ...
0
votes
0answers
13 views

WGCNA error in labeledHeatmap

I have a large RNA-seq dataset with multiple samples. I am doing network analysis using WGCNA. I got an error while making phenotype module relationship matrix. The code I am using: ...
0
votes
0answers
15 views

Seurat analysis only with matrix with no barcode and features

I have downloaded a dataset from GEO and only the matrix (mx) files are available. How can I perform the analysis without the barcode and the gene features?
0
votes
0answers
2 views

Can SBOL encode DNA Assembly linkers?

Where in an SBOL file could you specify the linkers that would be placed as prefixes / suffixes between parts for assembly? Lets say you have a final construct of your design and want to assemble the ...
1
vote
1answer
34 views

Multiple input & output files?

I'm trying to print out the measured distances for each .pdbqt file, and then write a new output file for each .pdbqt, using the original name of the .pdbqt file as the new .txt file name. Below is ...
3
votes
2answers
61 views

How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?

I would like to do two things: (1) Obtain a list of all NCBI (Entrez) gene ID's. (2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from ...
2
votes
2answers
30 views

Difference between isoforms and paralogs in transcriptoms?

I've assembled RNAseq data into a transcriptoms using Trinity. There's a option to keep only the longest isoforms for each transcripts and it lead me to wonder how it deals with duplicated genes (--&...
0
votes
1answer
48 views

Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes

I have raw paired-end RNA-seq reads for two novel eukaryotic species. Some background: the reads represent a copepod (arthropod) species each. The mRNA for each read set was obtained by extracting ...
0
votes
1answer
40 views

R not being able to find the file despite being in correct directory

I have question regarding a project I have to do about a health student study. I cannot import the csv file via read.csv or read.csv2 despite having transformed all files to csv and being in the ...
0
votes
1answer
20 views

Is it possible to predict protein-ligand binding kinetics using machine learning? [closed]

I would like to work on a project that involves the prediction of protein-ligand binding kinetics. What might be the feature that is relevant for the prediction?
1
vote
1answer
26 views

Relaxed and sequential Phylip format conversion

I routinely use AlignIO in BioPython for manipulating alignments and in context here moving from fasta format to phylip format. Alot of phylogeny packages accept a relaxed (sequence ID) & ...

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