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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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49 views

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 ...
0 votes
1 answer
72 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: ...
1 vote
1 answer
146 views

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 ...
1 vote
1 answer
34 views

R: 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 ...
4 votes
1 answer
66 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 ...
2 votes
1 answer
96 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: ...
3 votes
1 answer
89 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, ...
2 votes
1 answer
65 views

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 ...
3 votes
2 answers
70 views

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): ...
3 votes
1 answer
85 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. ...
3 votes
1 answer
34 views

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 ...
3 votes
1 answer
105 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 ...
0 votes
1 answer
82 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, ...
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 ...
1 vote
1 answer
40 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 ...
0 votes
1 answer
50 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 ...
1 vote
1 answer
30 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 ...
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 ...
1 vote
1 answer
156 views

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 ...
1 vote
2 answers
167 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....
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 ...
0 votes
2 answers
86 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 ...
1 vote
2 answers
73 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 ...
2 votes
1 answer
57 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 ...
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 ...
1 vote
1 answer
145 views

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 ...
1 vote
1 answer
77 views

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 ...
0 votes
0 answers
141 views

running fragpipe

I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
1 vote
0 answers
75 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: ...
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 ...
2 votes
1 answer
65 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 ...
2 votes
1 answer
84 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 ...
2 votes
0 answers
26 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://...
2 votes
1 answer
691 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, ...
1 vote
0 answers
20 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 ...
0 votes
1 answer
60 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 ...
2 votes
2 answers
129 views

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 ...
4 votes
1 answer
72 views

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 ...
-2 votes
1 answer
378 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: ...
2 votes
0 answers
70 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 ...
2 votes
0 answers
179 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 ...
1 vote
1 answer
53 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. ...
2 votes
1 answer
52 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 ...
-2 votes
1 answer
140 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 ...
1 vote
1 answer
58 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, ...
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) ...
2 votes
1 answer
109 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: ...
1 vote
1 answer
89 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 ...
1 vote
1 answer
75 views

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 ...
1 vote
1 answer
79 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 ...