Questions tagged [genomics]

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

Filter by
Sorted by
Tagged with
1 vote
1 answer
56 views

How to calculate distance between two regions from bed like dataframe in R?

I'm wondering how can I calculate the distance between two regions from the bed (chr, start, ...
Deb's user avatar
  • 183
3 votes
1 answer
55 views

What does the absence of a variant in a VCF file mean?

I have a individual.snp.vcf.gz file of an individual genome and the referencegenome.snp.vcf.gz file of the reference genome. ...
williantafsilva's user avatar
3 votes
1 answer
40 views

What is it about gene names starting with "LOC"?

I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
ToTheMoon's user avatar
0 votes
1 answer
67 views

Volcano Plot: How to show unique gene names in the plot?

I'm wondering how can I show unique gene names in the volcano plot. My data looks like, ...
Deb's user avatar
  • 183
0 votes
0 answers
15 views

Uploading manifest from CCDI to CGC project

Thank you in advance for your help! I am trying to download data from the CCDI (Children Cancer Data Initiative) and I have a manifest csv file that I downloaded from the CCDI. I'm trying to upload ...
msun5040's user avatar
1 vote
1 answer
32 views

What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?

This question was also asked on reddit Tries are a data structure that can be used to efficiently store and search for strings. Tries created from an ordered sequence of strings differ from the ...
GEP's user avatar
  • 111
0 votes
1 answer
48 views

Are there applications of semi-supervised learning to genomics?

Semi-supervised learning is when a portion of the training data set is labeled, and the rest is unlabeled; the unlabeled data is used to improved learning performance / accuracy. Are there (i.e., have ...
BigMistake's user avatar
2 votes
0 answers
59 views

How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: ...
DN1's user avatar
  • 45
1 vote
1 answer
28 views

Confirming Identity of clone in Phylogeny

This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole ...
prekij's user avatar
  • 13
1 vote
0 answers
25 views

What are some good miRNA databases?

I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein ...
Rachel Sweeney's user avatar
1 vote
0 answers
41 views

Does pooled sample genotyping microarray analysis exist?

I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches. With a higher sample throughput/volume, per sample cost becomes ...
BigMistake's user avatar
0 votes
2 answers
80 views

How to calculate average from a column when consecutive cells are similar in different columns?

I wonder how can I calculate the average of column 7 (WPS_win) when consecutive cells in column 2, column 3, and column 1 are the same. The file is in bed format (tab-separated format). The original ...
Deb's user avatar
  • 183
2 votes
1 answer
39 views

tensorQTL interaction issue

I hope that the question has its place on this board. I am trying to run the mapping of cis eQTL using an interaction term with tensorQTL. I am running into the following index error when running the ...
Solal's user avatar
  • 31
1 vote
1 answer
32 views

How to access yeast-cyc in a programmatic way to extract the GO terms?

I am a newbie in Bioinformatics, I want to extract the GO terms from yeast-cyc, which is items in the Go terms tab of this page https://yeast.biocyc.org/gene?orgid=YEAST&id=G3O-29622#tab=GO , not ...
Mountain's user avatar
  • 113
1 vote
2 answers
120 views

How to reverse complement a genbank file?

I am visualizing the alignment of a particular genomic region across different genomes with mauve. In certain genomes the region of interest is in the negative strand and in others the positive strand....
venkatesh war's user avatar
0 votes
0 answers
86 views

running fragpipe

I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
Mahendra Singh's user avatar
1 vote
0 answers
62 views

STACKS ref_map.pl no BAM records

I have 133 aligned and sorted BAM files that I am trying to run through the ref_map.pl script from the STACKS pipeline. My script looks as follows: ...
heather_l's user avatar
1 vote
0 answers
16 views

GenomicsDB and recalibration recommended for cohort of mixed exome (GATK)

We have a cohort of around 3k exomes, most of them from different capture kits, such as Agilent v6, v8, Nextera, Twist, Clinical Research exome and many others. Right now we are creating genome db on ...
Karthik Nair's user avatar
2 votes
1 answer
65 views

How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog?

How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog? For example, for PGS002723 (https://www.pgscatalog.org/score/PGS002723/), if I set ...
Cristian Riccio's user avatar
1 vote
2 answers
68 views

Extract data from genome

This question was also asked on Biostars 3 months ago, i.e. a long time - so its perfectly reasonable for the question to be asked here I started studying bioinformatics and I enjoy it a lot (I'm a ...
Sorin Trimbitas's user avatar
2 votes
0 answers
25 views

Nucleotide alignments from mmseqs "tblastn"

I am searching a protein sequences against a nucleotide database ("tblastn") using mmseqs and need nucleotide sequence alignments as an output. I start by the following (pg 23 of https://...
saladi's user avatar
  • 121
1 vote
0 answers
17 views

How Can You Reformat an OTU Table from qiime2 pathway to Include Sequence IDs?

I am trying to run Tax4Fun in MicrobiomeAnalyst, but am running into trouble with my table formatting. From the qiime2 pathway, I have an OTU, metadata and taxonomic table formatted like so: In ...
shannonevelyne's user avatar
0 votes
1 answer
58 views

What do the numbers mean in these RNA-Seq gene/transcript TPM files?

From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal ...
Macromind101's user avatar
-2 votes
1 answer
336 views

How to calculate Allele frequency from vcf file

Organism under investigation is Plasmodium falciparum. How to calculate the allele frequency for each row? I tried with this code: ...
skr3178's user avatar
2 votes
0 answers
154 views

STACKS: process_radtags only reads 1 input file and returns >90% barcode not found drops

I am trying to demultiplex some paired-end ddradseq data and am running into an issue with STACKS in that the program only seems to read 1 of my files for input (there are 2) and also results in over ...
heather_l's user avatar
2 votes
0 answers
67 views

Cut and Tag analysis

I am trying to do Cut and Tag analysis for a set of files and I want to perform a procedure called Tn5 normalization of samples. The basic goal is to generate bedgraph files and does normalization ...
Aranyak Goswami's user avatar
4 votes
1 answer
60 views

Identifying somatic mutations in cell lines

I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a ...
Macintosh's user avatar
  • 160
1 vote
1 answer
50 views

Transcript vs Primary transcript on phytozome

Could someone help me understand what the difference between transcript and primary transcript on phytozme is? For example, this dataset of A.thaliana has "primary transcript CDS" vs CDS. ...
Sudoh's user avatar
  • 217
2 votes
1 answer
47 views

Inconsistent replicate numbers in RNA-seq

I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake ...
Wang Ming's user avatar
  • 101
-2 votes
1 answer
111 views

How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?

I have performed genomic sequencing using nanopore technology and upon analysing using BLAST in the command line I have identified the presence of E.coli. I was wondering if I can add some code to ...
wilkohollie's user avatar
0 votes
1 answer
68 views

Mismatch between mutant gene and reference gene outside the site of mutation

I am tasked with designing primers for a particular mutant (Target Gene Locus: At1g28490 i.e. SYP61) of Arabidopsis, obtained from Gabi-Kat: The NCBI reference sequence for the genome goes: ...
AvadaMouse's user avatar
1 vote
1 answer
52 views

Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?

CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
ning's user avatar
  • 141
2 votes
1 answer
38 views

Using very closely related strains to increase coverage for short read, de novo assembly

Do you think it's possible to combine short read Illumina libraries (WGS) from multiple closely related eukaryotic microbial strains (e.g. libraries from a re-sequencing study, >99% ITS1 sequence) ...
bishopia's user avatar
2 votes
1 answer
94 views

Can I discard missing alleles?

I am converting a biallelic VCF into a SQL table and one of my tables will be something like: ...
glycoaddict's user avatar
1 vote
1 answer
87 views

How to identify sequence origin in DNA shuffle reads?

The data I have a large number of reads from sequences that were generated by randomly shuffling regions of two parent sequences together. See the following image: The regions that are shuffled are ...
Yano's user avatar
  • 13
1 vote
1 answer
77 views

Filtering reads greater than 5 from HT-seq count files

I have some raw counts from HTSeq after aligning with hg38 human reference genome. I want to do filtering in a way that the filtered count files should have the same number of lines. The reason behind ...
Aranyak Goswami's user avatar
2 votes
0 answers
90 views

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: ...
Aranyak Goswami's user avatar
2 votes
0 answers
117 views

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 ...
Anti's user avatar
  • 153
1 vote
0 answers
31 views

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.
julierebecca's user avatar
1 vote
0 answers
20 views

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 ...
Dev Desai's user avatar
1 vote
1 answer
38 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 ...
Balasubramaniam Namasivayam's user avatar
2 votes
1 answer
774 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 ...
Patrick Bastedo's user avatar
2 votes
1 answer
591 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, ...
Oludhe's user avatar
  • 21
2 votes
2 answers
209 views

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 ...
Gustavo de Miranda's user avatar
0 votes
0 answers
82 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 ...
Kumar's user avatar
  • 109
0 votes
2 answers
144 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 ...
Raz's user avatar
  • 1
2 votes
1 answer
64 views

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 ...
Angus Campbell's user avatar
1 vote
0 answers
35 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: ...
Kartika's user avatar
  • 11
2 votes
1 answer
369 views

Difference between bioinformatics and cheminformatics [closed]

Anyone can answer, and should be in simple way
Harsha's user avatar
  • 29
2 votes
1 answer
63 views

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 ...
aBiologist's user avatar