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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Nanopore sequencing continuation and data merging
I started a run which should last for 72 hours but unfortunately I had power failure and the remaining hours to complete was 31 hours. However, the base calling and bar coding will be done after the ...
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Converting Plink .bed files to .bcf *with* an AC (allele count) field?
I have some extremely large (N ~ 400,000) Plink .bed files that I want to phase using shapeit5.
Shapeit5 requires input data be in .bcf or .vcf format, and that it have an "AC" (allele count)...
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Disabling / Removing / Excluding / Collapsing * Allele SNPs indicating an Overlapping Indel
I am trying to find a way to disable the reporting of Spanning or overlapping deletions (* allele) within the GATK trio genotyping pipeline or a way to properly deal with SNPs given the ...
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Nucleotide diversity and TajimaD from SNPs
This question was also asked on Biostars
I have the illumina paired end reads of four chromosomes in fastq format. Using the cat command, I merged all of the fastq files into one. I used the GATK hard ...
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How to subset BAM file based on read length range (120-180) bp?
Hi I'm wondering how I can subset a BAM file based on read length. Precisely I want just read lengths of 120 to 180 bp reads in the new BAM file.
I'm trying several way, but none of them giving the ...
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How to measure mean of a column for every 10000 rows condition on other column?
I have a large bed-like dataframe with over 30 million rows. What is the best way to calculate the mean value of fourth column ...
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Creating custom VCF file
I'm stuck on what seems to be a banal problem, but I can't work out where the issue is. I need to create some customised VCF files that specify particular variants of interest.
This is a custom VCF I ...
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How do I summarise VCF files?
I have got a number of VCF files that all contain data on one particular variant, with every VCF being created from an individual sample. So there is one entry per file (headers omitted):
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How to extract all variant alleles that do not match "./." from the GT column of a vcf file?
For the two vcf files linked below, I cannot find any variants in the GT column other than "./.". Is it possible to confirm if the GT column of vcf files have been annotated (i.e variants ...
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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, ...
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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.
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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 ...
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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,
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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 ...
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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 ...
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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 ...
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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:
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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 ...
