Questions tagged [genomics]

Genomics is an interdisciplinary field of science focusing on the structure, function, evolution, mapping, and editing of genomes.

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Adapter trimming

I am trying to do adapter trimming, alignment and sorting for a range of large scale paired end fastq files. The code I am using is given below: ...
2 votes
0 answers
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Difference between pileup and mpileup in VarScan and samtools

I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan ...
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Transcriptome analysis

I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
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Compare illumina sequencing output with reference genome

I am new to whole genome sequencing. I want to compare illumina whole genome sequencing of mutants of a particular bacteria with a genome (not annotated) of the original strain to look for what the ...
1 vote
1 answer
27 views

Gene/protein expression specific to a group in omics

I am wondering what is the significance of finding a particular protein specific to a disease or control group? when we detect 1000s of proteins in a proteomics experiment, how can one be sure that ...
2 votes
1 answer
56 views

how to retain reads with low mapping quality (MAPQ) scores when using samtools view -q

I have been using the -q option of samtools view to filter out reads whose mapping quality (MAPQ) scores are below a given ...
1 vote
1 answer
60 views

Extracting base sequences from ABI/AB1 sanger sequencing chromatogram

I am trying to understand the sanger sequencing ABI/AB1 file format better, and extract base calls from given signal intensities over time. As I understand, reading in a raw AB1/ABI file into python, ...
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2 votes
2 answers
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BWA-mem and sambamba read group line error

this question has been asked [and answered] on Stack Overflow This is a two-part question: help interpreting an error; help with coding. I'm trying to run bwa-mem ...
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0 answers
25 views

Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?

I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
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0 votes
2 answers
48 views

what are the nodes and edges values in gene regulatory networks?

I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that explain how one can get ...
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2 votes
1 answer
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At what point is a gene different between species that we call it a different gene?

I am new to genetics and I know humans share many genes with mice for instance but that there are slight differences in conserved nucleotide sequences. Is there a community consensus around at what ...
1 vote
0 answers
25 views

NMF - Subscript out of bounds

I've calculated the cophenetic coefficients for the NMF of gene expression data, but is giving error when performing the clustering information step as given below: ...
2 votes
1 answer
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Difference between bioinformatics and cheminformatics [closed]

Anyone can answer, and should be in simple way
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1 vote
1 answer
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Statistical or performance test for genomic intervals between 2 samples

Is there an appropriate statistical or performance test to perform when I want to compare genomic intervals between 2 samples. Sample A is the the benchmark of comparing the intervals and sample B is ...
2 votes
0 answers
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How can I create a no-frills view config file for HiGlass?

Is there a basic example anywhere that explains how to create a no-frills view config to view the contact map for a non-human genome assembly using the server-based viewer at http://higlass.io? I ...
0 votes
1 answer
119 views

NMF clustering not giving results

I'm trying to run the Non-Negative Matrix Factorization(NMF) for my Gene Expression dataset which was originally in matrix form. But it throws errors as given below: ...
1 vote
1 answer
52 views

Transfer annotations from one genome assembly to another

I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length ...
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1 answer
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Mapping unique GO term description given a specific GO ids

I have a list of GO ids and I want to find out a unique term description such that if I provide say 200 GO IDs I will give 200 specific GO terms. The code snippet I am using is given below. Although ...
1 vote
2 answers
75 views

Counting the number of gene isoforms in a GFF3, is this method correct?

Recently I've been tasked to count the numbers of gene isoforms for each locus in a .gff3 file. I'm still doing my first steps in biology and bioinformatics, so I ...
1 vote
0 answers
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General Question: Statistical Alternatives to Oncoprint

I am a computational genomics student who has recently joined a research lab as an RA. We often work with oncoprints (comuts/heatmaps), and we visualize molecular signatures by reorganizing the comut. ...
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1 answer
38 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 ...
2 votes
1 answer
694 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 "...
1 vote
0 answers
137 views

How to modify dot plot in MUMmer 3 for bacteria comparative genomics?

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
1 vote
0 answers
174 views

Conversion of SAM to BAM files

I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file . The command I am using to make very ...
1 vote
0 answers
86 views

using Bowtie to map miRNA-seq data to rfam and also reference genome

I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code: ...
1 vote
1 answer
65 views

RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation

I have some transcriptomic (Whole) sequencing data that I should analyse. I would like to do raw data alignment to a reference genome taking into account the multi mapped reads and uniquely mapped ...
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1 answer
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How do you find differences when your metagenome sample size is small?

I received a matrix of genomics features (KEGG annotated metagenomes) abundance from 6 samples belonging to 2 groups. My collaborator is interested in finding differences between the two groups. The ...
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1 answer
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Converting FASTA Sequences to SNP FASTA Format

I have two FASTA sequences. Each is from a different species' mitochondrial genome. The sequences are pasted below. ...
0 votes
1 answer
31 views

how to get access to genotypes and phenotypes used for a GWAS

I'm a master's student working on genomic prediction of complex traits using deep learning. i'm looking for a dataset of human genotypes and phenotypes that has been used for a GWAS. The only thing i ...
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1 vote
2 answers
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Finding SNP/Indel Markers of Interspecific Variation

This is a revised version of my original question, edited to include the portions already answered by @Maximilian Press. Goal: Find SNP and indel alleles which are fixed between but lack polymorphism ...
1 vote
1 answer
209 views

How do I create a VCF file of all known pathogenic mutations in a gene of interest?

I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same ...
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0 votes
1 answer
106 views

Nvidia Parabrick fq2bam pipeline error - No such file or directory

I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for ...
1 vote
1 answer
70 views

How to count RNA sequencereads using custom made python scripts?

I am trying to do RNA seq analysis and my goal is to filter gene counts less than 5 using custom made python scripts. The code chunk goes as follows ...
1 vote
0 answers
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Genomic relationship matrix explanation

I am seeking the definition of the genetic distance matrices used in genomic prediction. What is the difference between a Rodger distance and kinship matrix? what people mean when they talk about ...
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Parsing PLINK recombination genetic map

I have a Plink genetic map with 4 columns: Chromosome, rs-snp, Map(cM), Position(bp) and approximately 8,000 lines find the recombination rate [Rate(cM/Mb)] from a HapMapII genetic map of 4 columns: ...
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1 vote
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How to extract certain genes including non-coding regions?

I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
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2 votes
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When to use Ariba vs Roary or other genomics tools to call drug-resistance variants?

I have a large dataset of assemblies of bacterial S. aureus genomes (~1000, same species). I am looking at different tools to estimate the presence of drug-resistance factors such as blaZ or ampC. ...
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3 votes
1 answer
662 views

What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?

Is there an accepted boundary of the extended major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 ...
1 vote
1 answer
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>My counter is counting genotypic combination occurences more than once, how do I ensure it counts one combination and doesnt count it again?

...
1 vote
1 answer
38 views

How to find Genotype, from list of mutations:lineage list?

I'm very new to python and I'm getting along nicely (I'd like to believe); however, I must be missing something here. I'm looking to read each and every file and compare each line against one another. ...
1 vote
1 answer
67 views

How to get % similarity between strains and mutation files

I’m very new to python, and having some difficulty getting hang of some more complicated things I have multiple files which look like so: hCoV-19/Singapore/4/2020|EPI_ISL_410535|2020-02-03 hCoV-19/...
1 vote
1 answer
81 views

How to identify unknow bacterium species from whole genome genetic sequence

I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole. I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled ...
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1 answer
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Pointing Cromwell to local EBS mounted storage on AWS Batch

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend. I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
2 votes
1 answer
112 views

COVID-19 GWAS: what is a cross-replicating association?

In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, ...
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1 answer
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How to annotate gene length to a list of gene symbols using UCSC data?

I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
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1 vote
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"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
1 vote
1 answer
65 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
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2 answers
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How identifiable are human omics data and how to mitigate their identifying features?

Say a database were to store human omics datasets. The human subjects are known and the sample size is rather small in size initially (n=500). The database contains genomics, transcriptomics, ...
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1 answer
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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 ...
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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.