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Best practice for running GATK VQSR on X chromosome

According to GATK best practice, it is recommended that different VQSR models be built for SNPs and INDELs, because the annotations for high-quality SNPs and INDELs are systematically different (if I ...
0
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1answer
17 views

calculating kmer nucleotide frequency per column

I have a list of sequences: CAGGTAGCC CCGGTCAGA AGGGTTTGA TTGGTGAGG CAAGTATGA ACTGTATGC CTGGTAACC Each sequence is nine nucleotides long. I want to calculate ...
2
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0answers
15 views

How to use SRA Toolkit to blast SRA accessions?

I'm trying to look for a gene in a group of SRA files. Web BLAST can't cope with them, so I assume they're too large. I've tried tblastn_vdb from the SRA toolkit, as follows. It had previously worked ...
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0answers
22 views

converting mouse genes to human genes

I'm trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I'm using this file for the orthologs. http://www....
0
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1answer
22 views

loading in .txt files with different spacing in column names into R

Trying to read in this file but saved as a .txt file: http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt ...
-1
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1answer
29 views

TCR-seq or scRNA-seq

I need idea, intuition, suggestion please I have 10X scRNA-seq of PBMC (multiome's 3' poly-A capture), can I capture ...
1
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0answers
10 views

FoldX PositionScan functions only works for certain position inputs

I'm using the PositionScan function in FoldX 5.0 to calculate delta delta G for some mutants. I'm working with the command prompt in Windows 10. For some reason, this function will only return output ...
1
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0answers
9 views

Counting the number of occurences of variant A or B, or A and B on a sequencing read

I need some help getting started on this project. To simplify we want to be able to quantify the occurence on 3 variants on each sequencing read in an alighnment file as a proxy measurement for ...
0
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0answers
18 views

Getting all promoters of a specific gene

I'd like to perform a motif analysis of all promoter regions of the gene ENSMUSG00000020538 in mus musculus. To do so, I wanted to use Biomart : ...
0
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2answers
52 views

Question about the practical relevance of chromosome position and p-value

Article of interest: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/#SD1 Referring to Figure 2b of that article, if I understand correctly, the x-axis refers to the position of each variant in a ...
0
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1answer
23 views

How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?

I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
1
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1answer
31 views

shiny dashboard to visualise RNA seq data

I am trying to build a shiny dashboard for the visualization of different RNAseq data sets. However, I am encountering problem with reactive input, the code is always using the second dataset that I ...
0
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1answer
37 views

Beginner with DESeq2 having issue with analysis

Hi there I am brand new to using RStudio and trying to run DESeq2 analysis on my featureCounts output counts table. I ran the following code: ...
0
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1answer
22 views

Sample versus subject in scRNA-seq

I am reading this paper, where the authors mention We apply SAUCIE to the batch correcting, denoising and clustering of an 11-million cell mass cytometry dataset with 180 samples from 40 subjects in ...
0
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1answer
20 views

How to use multiple .pdb files as templates for homology modelling?

I just ran an AlphaFold job for PduK from the Pdu BMC operon and got very strange results including a large circular loop of random coil. According to Mayer et al., PduK should be semi-triangular ...
0
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0answers
27 views

Is it possible to add one more sample to the result of featureCounts?

I have some .bam files and I also got featureCounts by Subread. But after getting the featureCounts I realized that among my bam files 2 of them actually belong to the same sample. So I wonder if I ...
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1answer
23 views

Is it normal to have a smaller bam file after merging bam files?

I have 2 bam files that belong to the same sample and I merged them with samtools merge. And after merging, I realized that the merged version is a bit smaller than ...
0
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0answers
39 views

Making a box plot of the proportion of cells in each cell types in two groups

I have number of cells in three cell types T, B, M in a Seurat object For two groups of patients, cancers and controls like ...
1
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0answers
24 views

How to interpret scRNA-Seq cell dynamics from scVelo and CytoTrace results

I have the following scRNaseq analysis done with scVelo and CytoTrace. My understanding is as follows: scVelo arrows lead from less differentiated (more stem cell) to more differentiated (e.g. ...
2
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0answers
28 views

Splice variant analysis with ensembl genome/annotation/rna. Which files do I use?

I am running splice variant analysis. I wanted to use NCBI genome but the program works better with ensembl. I am a bit confused on primary vs. top level to use as my reference genome. I also do not ...
-1
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1answer
55 views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
0
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1answer
24 views

Parallelizing microRNA targets

I am trying to look for miRNA targets using a file called Conservedfamily.txt from the Zebrafish target scan fish website. I have written a python program to ...
0
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2answers
51 views

Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
2
votes
1answer
23 views

SCTransform Warning: in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Running SCTransform on my seurat object produces the warning: Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached What does this warning mean? ...
0
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1answer
18 views

Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?

I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
0
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1answer
35 views

programmatically select and label peptides within pdb file

I have a pdb file of a protein structure, and I would like to programmatically select certain peptides and label them in an annotated pdb file output, so that when the output pdb file is opened again ...
0
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1answer
47 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
1
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1answer
51 views

How to download data from SRA in Linux systems via the command line?

My workflow for downloading data from SRA has been the following: Access SRA Run Selector. Enter the accession number for the project of interest. Download "Accession List" for the "...
2
votes
1answer
37 views

DESeq2. Which is better: using the altHypothesis argument in the results function or manually filtering for your desired P-value and Log2FoldChange?

In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab using the results() function with the minimum number of arguments supplied (...
1
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0answers
29 views

Doing functional enrichment of microbiome data

I have done gene set enrichment analysis which is now straight forward. Such as taking gene set and making a query. For microbiome data it is not that straight forward which I found out. Step done so ...
2
votes
1answer
19 views

How to download the whole genome of an organism from NCBI using R or Python?

I need to download some of the genomes of human gut microbiome in FASTA format. Anybody has any script to download?
3
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1answer
53 views

How are tertiary protein structures represented in computers?

What data structure is used in representing protein structures in computers so that we can apply algorithms? Matrix or Graph or tree? P.S. I am absolutely new to Bioinformatics.
0
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0answers
58 views

Python script to calculate properties of amino acids and storing them in matrix

I want to make a python script that can get as input sequence of N amino acids, and the output is a matrix of Nx6 containing 6 features. The features are: Computed volume Hydrophobicity Polarity ...
0
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0answers
64 views

hclust error - Formula must be of the kind “~A1/A2/…/An” [closed]

I am getting an instant error with Clustermap R package which I think relates with another packages ...
1
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0answers
28 views

How to quantifiy of specific genes from shotgun metagenome?

I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
2
votes
1answer
58 views

Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to ...
0
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1answer
24 views

Error when trying to move multiple file types in wdl

I tried to add a "gather_results" task to a workflow that takes in an array of Files and moves output files to a new folder of a specified name. ...
-1
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0answers
26 views

Dimplot does not show the same cell IDs

I have downloaded raw read counts and cell type annotation (cluster number and cell type related to each cell IDs) from a paper By raw read count I made a seurat object ...
0
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2answers
52 views

Merging two dataframes in R

I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like ...
-1
votes
1answer
36 views

Filtering cells from values in metadata

I metadata slot of Seurat object I have mapping score of each cell to a reference PBMC data like ...
0
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1answer
36 views

What does this Seurat argument mean

I have extensively read about percent mito in Seurat but I got more and more confused Let's say we want to keep cells with ...
0
votes
1answer
44 views

Seurat Dimplot with different clustering IDs

In Seurat metadata I have assigned cells to some cell types with different resolutions I have added the cluster identities to the object via Idents: ...
0
votes
2answers
42 views

Remove from Multi-FASTA by Sequence ID

I want to remove sequence VRE32514 – it doesn’t belong and thus is the reason it lacks additional metadata. However I tried implementing this code from a similar question: ...
0
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0answers
13 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript. We used ANGSD to calculate Thetas, Tajima and Neutrality tests and one of the thetas was a pairwise theta, however I am ...
0
votes
1answer
12 views

BEAUti not accepting taxa tip dates

I'm using BEAUti as part of my pipeline and the sequence names include | to separate the metadata fields - with culture date being at the very end. When I attempt ...
0
votes
3answers
55 views

The confusion of using TPM (transcripts per million)

It is shown that TPM values are not suitable for DEG analysis but good for within-sample comparison since TPM normalized the gene length. My question is first: if TPM is not suitable for across ...
1
vote
0answers
26 views

How to choose the proper way to analyze the differential binding peaks among different samples for ChIP-seq? DiffBind or CSAW?

I have used the TMM method in CSAW package to normalize the composition bias for my different ChIP-seq samples and also got the normalized bigwig files. Next step I want to analyze the differential ...
1
vote
1answer
19 views

A unified database for CNV, SNP, Indel and MSI

I am looking for a database or different databases where I can find information on different gene variants for a gene. As an example if I enter PPARG, I could be able to see SNPs, CNV, InDels and MSI. ...
1
vote
1answer
17 views

Trinity assembly from many samples

When you combine samples for de-novo transcriptome assembly with Trinity, do you suggest limiting the number of reads for each sample? I had read one of Matthew MacManes' papers awhile back suggesting ...
0
votes
2answers
70 views

Converting a matrix array to matrix

I have a matrix in R. When I run class(my.matrix) it returns: "matrix" "array" Why do I get "array&...

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