# All Questions

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### DNA sequence error annotation

Suppose I generate a DNA sequence of the following pattern. AAGTC And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence AAAGGC Where ...
10 views

### Detecting Allelic Imbalance

I am interested in detecting allelic imbalance for a credible set of SNPs. Currently, I am looking for some packages, hopefully, for Python, that can assist with this. I am aware of this R package, ...
10 views

### How do I lift GWAS results to hg38?

There are some questions about lifting between reference builds, e.g. this one. But there doesn't appear to be a question about lifting a GWAS results file to a new reference build (except off-site). ...
11 views

### Is is possible to predict ncRNAs from sequence and homology alone?

I'm working with a set of homologous genes (let's call it gene A) from several bacterial species. I know (from previously published research) that in gene B (a close paralogue of gene A), there is a ...
23 views

### Rejected publication [closed]

A publication that we have been working on for over 6 months on COVID-19 has been rejected by 2 journals. The objective of our research was to identify effective compounds against the COVID-19 virus ...
15 views

### FASTA and PDB: How to specify chain?

For proteins that have multiple chains (e.g., 1EMS), is there an easy way to specify which chain I want to use for blastp? I cannot imagine that I am the first person to have this problem, but so far ...
41 views

### How does Allele Number get determined in VCF files?

I am looking at the publicly available gnomAD v3 VCF file. The header describes the AN field as: "Total number of alleles in samples." This suggests to me that it should be a constant ...
10 views

### Are there other currently available codon bias indexes , other than Kaks, to distinguish between positive and negative selection?

I am currently dealing with the study of T.gondii's proteome. I downloaded the complete set of CDS from NCBI GenBank and I am now starting to decide how to implement the analysis. I'm pretty ...
38 views

### How would we test for significant changes in expression when many of the normalised counts are clustered together?

I've been handed RNA-seq data with a lot of associated covariates. This data has been put through the DESeq2 package and as a result normalised the data. One of the transcripts of interest still has ...
28 views

### Assessing PyMol sequence alignment object

I use cealign in PyMol for structure alignment. Instead of visualization, I want to return the alignment object to my python script for further analysis. Is there a function to return the object ...
41 views

### How to replace sequence identifiers in a fasta with OTU IDs from another file?

I'm pretty new to Unix and bioinformatics and having a hard time accomplishing the following. I have one FASTA file with sequences and headers, and one OTU ID mapping file (.txt) with OTU IDs and ...
26 views

### How to print alternative allele from VCF with htslib c++

I would like to print the alternative allele from a vcf file which i load in with htslib. The description of some functions: https://github.com/samtools/htslib/blob/develop/htslib/vcf.h I have used ...
37 views

### How to remove duplicates from a fasta file using python

I am using the following command: ...
22 views

### How to obtain desired output?

I am working on a project using the following command within nano: ...
40 views

### How to fix NameError?

I am working on a project and am having issues with the following code that I have written in nano: ...
15 views

### Convert sequence in MS doc to fasta or genbank

How can I convert a sequence provided in a Microsoft doc file into a fasta or genbank format?
18 views

### How to choose docking score cutoff?

I made a virtual screening of a large database (~5M) and want to filter ligand structures for further more accurate screening (from Schrodinger HTVS to SP resolution). My next step is to define a ...
33 views

### Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

Here I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question... Here result that one Bat Sars coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(...
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### What datasets are available out there for prediction based on DNA sequences? [closed]

I am looking for publicly available data for a genomics deep learning project. My goal is to compare different architecture to predict biological insights from DNA sequences. I have heard about Janggu ...
35 views

### Plot information stored in dataframe within a tree (ggtree)

Hello to the entire Stackoverflow community! I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one: df : ...
21 views

### Moving UMI from tag into read name

I have a bam file with Unique Molecular Identifiers (UMIs) for each read present on the RX tag ( such as RX:Z:TGAGAAGGG), as expected by picard and fgbio tools. ...
15 views

### I have used TER to break the long bonds of a chain in my PDB

I’m now not sure what I need to alter in my PDB to get it to work in leap. I know breaking the bonds turns the formerly connected residues into terminal residues. It keeps saying that 3 of my atoms no ...
8 views

### Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
21 views

### How do you visualize minimap2's PAF output format?

As described by the developer of minimap2: PAF is a text format describing the approximate mapping positions between two set of sequences. He also suggest to use either Ribbon to visualize PAF files,...
27 views

### How to count the kmer occurrence in FASTA file considering overlapping and reverse complement?

I am using count_overlap() for counting the kmers from Biopython . Does it take the reverse complement of kmer into account? I need to count reverse complement too
18 views

### Where can I find Python code for progressive sequence alignment? [closed]

From the title. I am learning about multiple sequence alignment and would love if someone can link me an in-depth walkthrough on how to code for a MSA using progressive sequence alignment by using ...
15 views

### Get dataframe from an LipidomicsExperiment when using lipidr package

With the library lipidr lipidomics data has been normalized using the function normalize_pqn(), and I need to get the normalized data to perform further statistical ...
15 views

### How to analyze the correlation of two different tissue gene expression under three conditions?

I have three conditions A, B, and C. For each state, I have gene expression data of two different tissues(liver and pancreas). I am studying the possible network/correlation/ between tissues for each ...
18 views

### Chip-seq down-sampling problem

Control sample chip read stat ...
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### What number to give for -ploidy for durum genome in GATK?

I have some genome sequencing data from durum wheat. I'm using GATK to call variants. I got the genome sequence here: http://plants.ensembl.org/Triticum_turgidum/Info/Index Here is the reference ...
8 views

### how do we interpret enrichment score in xCell?

I need some help in interpreting the results produced by xCell. I cannot find information about interpreting the results. For example a enrichment score of 0.005 in a cell type (eg basophils) in a ...
4 views

### ConsensusClusterPlus for sample classification

Many large studies like TCGA use consensus clustering for transcriptional subtype identification. The most popular package for that seems to be ConsensusClusterPlus. If you want to classify an ...
16 views

### Marking Alignment sequences - Mark mutations of interest [closed]

Just wondering if there is any possible programmes which will allow me to mark amino acid mutations of interest on a sequence alignment. The only way I can currently think of is through Moffice, and ...
26 views

### Measure the purifying selection for certain taxa along a phylogeny

I am posting this message because I need clarity about the analysis I want to perform. In my analysis, I have a homologous gene in 13 species, and I would like to evaluate the selection pressure of ...
21 views

### Tools to find similarity and identity via terminal or ubuntu [closed]

Which tools to find similarity and identity via terminal or ubuntu, more complete and with better results? What are the tools to have a quality control of the alignments? That can run from the command ...
23 views

### Does BLASTClust guarantee that proteins in different clusters are dissimilar?

I need to find dissimilar proteins. Looking through the PDB I found the weekly BLASTClust results of proteins that are 30% similar. However, I do not know if protein A in cluster 1 is guaranteed to be ...
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### How to annotate ChIP peaks base on NCBI sequence name?

I have chip-seq peaks based on NCBI genome which looks like the following: ...
51 views

### Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function ...
50 views

### If a gene is expressed at a level of 1/1200 compared to the average gene, how is probability 50:50 that we have a read mapped to it?

I am reading a book about RNAseq analysis and it says "To calculate the probability that a read will map to a specific gene, we can assume an average gene size of 4000 nt (100 M nt divided by 25,...
27 views

### How to concatenate two fasta sequences by py

I have three backbone and i want to concatenate 70 sequence into these backbone. such like: fasta file 1: ...
4 views

### Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
17 views

### How do you calculate the top L/5 score?

I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...
22 views

### Comparison of phylogeny of SARS2 whole genome vs spike genome

This is more of a general bioinformatics question, not any coding required. So I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files. My next step is to compare ...
22 views

### Random GWAS data generator

I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
32 views

### RAD Seq Data Analysis without barcode

I received a ddRAD Seq data from my supervisor without barcodes and restriction enzymes. I asked him for both and he said I don't need it since the data has been cleaned by the company. Now, I am ...
8 views

### how to get out full length transcriptome sequence from string tie assembly data? [closed]

I have started work from reference guided assembly to make with raw read(RNA seq) and the reference genome. I got string tie assembly data ( GTF format). I will need structural and functional ...
46 views

### Merging several fq.gz files or R1 and R2 classes into a single one

I have the following files: ...
13 views

### annotation using ChIPseeker package error

I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
33 views

### How to remove batch effect from TCGA and GTEx data

I want to play some differentially expressed genes for gliomas cancer. I collected cancer tissue profiles from the TCGA database and normal tissue profiles from the GTEx database. I straightforward ...
65 views

### How can I subset WGS data to the level of WES variants?

I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...

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