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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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 ...
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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....
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running fragpipe
I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
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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:
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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 ...
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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 ...
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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://...
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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 ...
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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 ...
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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:
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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 ...
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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 ...
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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 ...
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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.
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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 ...
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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 ...
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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:
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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, ...
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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) ...
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Can I discard missing alleles?
I am converting a biallelic VCF into a SQL table and one of my tables will be something like:
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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 ...
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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 ...
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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:
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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 ...
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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 ...
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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 ...
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416
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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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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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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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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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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 ...
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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:
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309
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Difference between bioinformatics and cheminformatics [closed]
Anyone can answer, and should be in simple way
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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 ...
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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 ...
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202
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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:
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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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Mapping unique GO term description given a specific GO ids
This question was also asked on Biostars
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 ...
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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 ...
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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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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 ...
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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 "...
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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 ...
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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 ...
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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:
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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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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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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.
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