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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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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What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
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 regular Tries in the following way:
If there ...
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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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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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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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Genomics: Downloading genomic data from the NCBI Genbank database
I'm taking a genomics course at school, and we have a final project due in a few weeks.
Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
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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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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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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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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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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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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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Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset
First of all, I'd like to apologize for any spelling or grammar mistakes.
I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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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 ...
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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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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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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 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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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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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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Genomics Statistics Problem
I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding.
I have identified 728 sequences of interest. 597 of these ...
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Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?
Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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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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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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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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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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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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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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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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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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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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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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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
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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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