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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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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
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2 votes
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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://...
saladi's user avatar
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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 ...
heather_l's user avatar
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 ...
Aranyak Goswami's user avatar
2 votes
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92 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
133 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
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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 ...
Rotwurg Nwossle's user avatar
2 votes
0 answers
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When to use Ariba vs Roary or other genomics tools to call drug-resistance variants?

I have a large dataset of assemblies of bacterial S. aureus genomes (~1000, same species). I am looking at different tools to estimate the presence of drug-resistance factors such as blaZ or ampC. ...
Soerendip's user avatar
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2 votes
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What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
mRotten's user avatar
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2 votes
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148 views

How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
Ahmed Abdullah's user avatar
2 votes
0 answers
157 views

Meaning of category in MutSigCV

I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
Lot_to_learn's user avatar
1 vote
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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 ...
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
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: ...
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
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 ...
shannonevelyne's user avatar
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
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21 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
0 answers
37 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
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1 vote
0 answers
25 views

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. ...
dunkindonts's user avatar
1 vote
0 answers
451 views

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 ...
HelpNeederStudent's user avatar
1 vote
0 answers
864 views

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 ...
Aranyak Goswami's user avatar
1 vote
0 answers
211 views

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: ...
user12371's user avatar
1 vote
0 answers
63 views

Genomic relationship matrix explanation

I am seeking the definition of the genetic distance matrices used in genomic prediction. What is the difference between a Rodger distance and kinship matrix? what people mean when they talk about ...
snowflake's user avatar
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1 vote
0 answers
91 views

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: ...
Lar's user avatar
  • 11
1 vote
0 answers
134 views

How to extract certain genes including non-coding regions?

I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
Soerendip's user avatar
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1 vote
0 answers
40 views

"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
Pragati Bhingare's user avatar
1 vote
0 answers
444 views

How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
Kyle Weise's user avatar
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 ...
Giannis Lazaridis's user avatar
1 vote
0 answers
145 views

Colinearity analysis with respect to gene orientation

I was reading the manual of MCScanX and found that besides a all-vs-all protein blast file the tool takes a gtf file with four columns only: scaffold name, protein name, from, to. As the tool is not ...
Kamil S Jaron's user avatar
1 vote
0 answers
66 views

Complete Genomics Junction file for SV Detection

At present, I have vcf file for each patient generated from tumor data. I am using virtual normal correction method for somatic mutation detection because I don't have normal data. For SNP or small ...
Lot_to_learn's user avatar
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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
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?
Mahendra Singh's user avatar
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: ...
AvadaMouse's user avatar
0 votes
0 answers
87 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
-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: ...
skr3178's user avatar