# All Questions

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### merging two/or more bed file into one bed file

I am trying to merge two bed files (more in future) to one. my bed files are something like : . I need to merge them in a way to have the shared chromosome location. Is there a way to do that ?
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### Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

After performing BLAST searches, I identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while gene Y ...
10 views

### umap highlighting two different models

I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap to where it shows the umap with the different clusters but I want to show where the ptx samples ...
7 views

### How to compute module completion ratio of KEGG modules from KO identifiers? (command line)

I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I'm ...
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### co-localisation error code using co-loc

Can anyway advice on what the below error code relates to. I am using co-loc R package with 2 GWAS datasets. Using coloc.abf function with pvalues, MAF, sample size and case/control cohort. Thank you ...
35 views

### Calculating the number of probes for a given genomic range

I have a big data frame like this for copy number (exome seq) ...
18 views

Between the qvalue package and the p.adjust function, which is more appropriate to use when trying to calculate the q-values of a dataset? According to the manual for the q-value package, the q-value ...
63 views

### Allele count is zero

I ran freebayes on bacterial data and got a vcf file. Some of the SNPs found have AC=0, but in the bam file I can see that there are alternative alleles, so in my ...
30 views

### Running a script in python

I am trying to run a script in python but I getting this error ...
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### Does the Abbott coronavirus test pick up the virus if you are still in the incubation period? [closed]

It seems like Abbott's ID Now test works by detecting the virus directly as opposed to checking for antibodies? If the test result is negative does that mean you don't have the virus? Or does that not ...
10 views

### nextflow fromPath not passing all files with *

main.nf is #!/usr/bin/env nextflow params.input = '' tchan = Channel.fromFile(params.input) tchan.println() I have a.bam, b.bam and c.bam I run: ...
30 views

### truncate fastq.gz file without error in Snakemake

All, As the first step in my Snakemake pipeline, I generate small fastq files from all input fastq.gz files. This is to run a quick round of "infer_experiment.py" (from RSeQC, to get the kit ...
16 views

### Can I pull a jackhmmer output file into ClustalO for pairwise alignments?

I'm still working on figuring out how to send ClustalO multiple jobs. I have a hmmer output and was looking to do a mixture of pairwise and local alignments on a subset of these. Is it possible to ...
21 views

### Is there a aminoacid mutation that forms similar protein?

Is there an amino-acid shift that will 99% of the time end up resulting the same biochemical function/structure and implications?
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### How to identify where the mutation occurs frequently

I currently have 2 fasta files with 139 sequences. One that is already aligned and one that is not. Each file is Sars-cov2 sequence file from ncbi. I was wondering what I can do to find locations ...
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### Understanding some of the computational bottlenecks of Covid-19 research

I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of softwares used for ...
44 views

### Merging based on Chromosome coordinates

I have a simple task which seems very complicated now Two data-frame I have One contains the Chromosome coordinates of distal enhancer elements and other one rlog values of accessibility which I want ...
38 views

### How did researchers derive the Ramachandran “validation” contours?

I'm a beginner to structural biology and for fun, calculated the tortional angles of some 100, 000 proteins. Here is my Ramachandran plot: When I went to look for "canonical" Ramachandran plots, I ...
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I am new to the field of Bioinformatics. GTEx database is great; I know how to check whether a SNP is eQtl with the online tools of GTEx. But my question is how to download the right data to draw a ...
22 views

### Phasing partially phased genomic data

I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since ...
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I am downloading sample slides (in svs format) from the GDC Portal for a convolutional neural network model, but I also need normal tissue slides. There are some normal tissue slides that are adjacent ...
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### Cuffmerge: [Samtools-help] EOF marker is absent. The input is probably truncated

I need to merge my all transcripts.gtf from cufflinks output follow this command line : cuffmerge -o merged_gtf_output -p 15 -s ref.fasta -g anot.gtf assembly.txt but I have this warning : [...
19 views

### How to find the region with frequent mutation?

I am very new to bioinformatics and I was wondering if I can get some help regarding finding region that has high mutation rate. Currently, I have 2 fasta files, one that is aligned and one regular ...
22 views

### Coding object structure properties into a sequence

Hopefully, I found the right place to ask. Please, note that I'm not a specialist in the current field. Is there an algorithm to code information about object structural properties into a sequence (...
43 views

### Analyzing proteins based on sequence similarity

Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic ...
13 views

### Software for microbial profiling from 16S rRNA gene sequence

I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
43 views

### How can I understand FASTA sequence of Coronavirus? [closed]

In GenBank it is mentioned that the COVID-19 virus has an RNA genome, but here in the community someone wrote that it is cDNA and not RNA. For translation RNA must contain a start codon and poly A ...
15 views

### GWAS, MWAS, EWAS: what are the (in)dependent variables?

I started reading some papers on X-wide association studies, where X can be metabolome, epigenome, etc... The authors usually describe which are the dependent and which are the independent variables ...
19 views

### Feature extraction methods that can handle inconsistent numbers of atoms for molecular dynamics

I want to compare the protein dynamics ) pH 7 versus pH 3, or ) wild type versus mutant The protein will have slightly different number of atoms at each condition, due to protonation or mutation, ...
113 views

### Are the conclusions in “The proximal origin of SARS-CoV-2” legit?

I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
17 views

### Marking opical or PCR duplicates with picard vs. samtools flagstat

I am trying to identify the best library prep method for noninvasive prenatal test samples, to be sequenced with Illumina Novaseq. One metric that I am evaluating is the number/ percentage of PCR or ...
14 views

### Query regarding beta value imputation

I am trying to do differential methylation analysis (DMA) using limma package. I have downloaded the Illumina 450k array data from GDC database and pulled out the data for required probes. I have ...
13 views

### Filtering genes from cuffdiff results

I have run cuffdiff (with statistics turned ON) to compare two groups of samples: Control group and Late AD group. This is the command I ran to be precise: ...
18 views

Please, can you help me with a confusion? In whole genome sequencing, if Total copy number (major + minor allele copy number by SCAT R package) for SMAD4 in a ...
35 views

### Overlap in Paired-end Reads for Sequencing?

Regarding Sequencing: Do/can the paired-end reads have overlaps?
65 views

### Can I automate CLUSTALO and output alignment sequence identity?

I've detected homology between targets of ligands in drugbank and proteins in the proteome of a pathogen. I've parsed the output very rudimentary and calculated my query coverage. This exists in an ...
9 views

### Batch annotation with RAST

I have been looking into ways to batch annotate my bacterial genomes via RAST, however I cannot access the tutorials on blog.theseed.org as my browser prevents connection for security reasons. Does ...
43 views

### Location of Reads in Sequencing

I have questions regarding sequencing: Are paired-end reads from different stands? What about single reads, are they coming from both strands?
11 views

### Logit-normal distribution to model variation among biological replicates

I came across rMATS while doing research on differential alternative splicing (AS). It uses logit-normal distibution to model variation among biological replicates. I am having difficulty ...
29 views

### Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?

I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to ...
4k views

### Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]

I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type ...
28 views

### Warning in fastqc

I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of ...
65 views

### What is the difference between fixed effects and random effects in the context of Linear-mixed models?

The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
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### CRISPR Screen Control - What genes do not affect phenotype when knocked out?

I have some raw read count data from a crispr screen. The library used was addgene's Mouse Improved Genome-wide Knockout CRISPR Library v2 I'm following an ...
30 views

### How to compute Shanon entropy

I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
27 views

### Per Base Sequence Content in fastqc

I have a question regarding "Per Base Sequence Content" plot for "fastqc": In the fastqc documentation, it is written: "In a random library you would expect that there would be little to no ...
17 views

### Generate VCF from different .bam files with different chromosome names

I have two resources of .bam files. One is generated by our lab (1 sample = 1 bam). One is downloaded online (again 1 sample = 1 bam). For the downloaded samples the chromosomes are labelled: chr1, ...
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### How can I match gene IDs from different platform?

I have two sets of GSE from GEO database and I would like to develop a prediction model in one set and velidate the model in another set. How can I match the gene names? The code are enclosed below. <...