Questions tagged [software-recommendation]

Questions asking whether a software exists for a certain purpose; questions asking which software is best among a selection for a certain purpose.

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13 views

Is is possible to predict ncRNAs from sequence and homology alone?

I'm working with a set of homologous genes (let's call it gene A) from several bacterial species. I know (from previously published research) that in gene B (a close paralogue of gene A), there is a ...
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2answers
65 views

How can I subset WGS data to the level of WES variants?

I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
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19 views

MM/PB(GB)SA calculations for DESMOND trajectories

I did molecular dynamic simulations with DESMOND. Now, I want to obtain the interaction free energy using MM/PB(GB)SA. The free tools I found to perform such calculations are AmberTools and g_mmpbsa. ...
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39 views

Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
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24 views

Gene Ontology equivalent - higher specificity?

I've recently discovered OrthoVenn2, which I'm using to compare proteomes and extract likely clade-specific genes. I'm enjoying software, and one of the things it offers is a breakdown of protein ...
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19 views

Free, user-friendly software for visualizing and comparing gene clusters?

I'm looking for a tool to do the job listed in the title. I've come across Gene Graphics (https://academic.oup.com/bioinformatics/article/34/8/1406/4708234), but never used it and I was wondering if ...
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93 views

Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!

I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data. I have the file contigs.fa from short reads but phasing step with ...
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2answers
158 views

Understanding some of the computational bottlenecks of Covid-19 research

I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of software used for ...
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33 views

Software for microbial profiling from 16S rRNA gene sequence

I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
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3answers
208 views

Is it possible to do this in R?

I have a big clinical data file with 96 columns like age, gender, BMI, etc I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
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2answers
128 views

What assembler is appropriate for High-Fidelity PacBio reads

What assembler is appropriate for High-Fidelity PacBio reads? For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the ...
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1answer
174 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
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2answers
154 views

How can I transform a mapped BAM file into an unmapped BAM file?

In order to use MergeBamAlignment (Picard), I need an unmapped BAM file and a mapped BAM file. I have two mapped BAM files: one with reads mapped to the reference I want but without metadata such as ...
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1answer
33 views

Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
3
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1answer
54 views

Detecting broad peaks in sRNA-seq data

What kind of tool would be appropriate do detect "broad peaks" in small RNA-seq sequencing data? MACS2 appears to be developed for ChIP-seq data, but I see that there is a ...
3
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1answer
86 views

programmatic secondary structure prediction for >36-mer DNA oligonucleotides

I'm writing a tool to automate Sanger sequencing primer design for a production lab that uses a universal-tail chemistry Sanger sequencing to verify NGS results. Essentially, the template DNA is ...
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76 views

How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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15 views

Iupred definition of long/short form disorder

I need to predict disorder of proteins and here there is a description of Iupred in its two variants, long and short-disorder. This is a manuscript defining the method. I couldn't find a precise ...
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2answers
310 views

Plotting coverage of annotation over collection of region

I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in ...
5
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2answers
446 views

full visualisation of draft genomes alignment

I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (genome1.fasta) and one with ~1'000 contigs (...
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1answer
134 views

Exporting nt's differences from MEGA alignment

I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs ...
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81 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 ...
2
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1answer
61 views

Is there an R package that computes homoplasy excess ratios (HER)?

I want to calculate the homoplasy excess ratio for a phylogenetic tree, for example homoplasy resulting from recombination. I am wondering if there are any R packages out there that will do this?
4
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1answer
335 views

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

The dilemma: I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads (both pacbio and ONT). ...
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50 views

case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
8
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1answer
88 views

Best practices for deciding if two structural variants are actually the same variant?

I know that I can use bcftools isec to compare two VCF files containing single nucleotide variants (SNVs); it will generate four possible output files: one with all ...
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2answers
101 views

Deciding which samples go in which batch

I have 370 samples to sequence, we probably will end up using only 96 samples per run (due to the barcode with the primers we'll use). This means running 4 batches. To minimize the batch effect I need ...
8
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2answers
1k views

estimate genome size: kmer-based approach from PacBio reads

Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)? Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
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84 views

Detect gene duplication events from a whole genome in FASTA format

Are there any tools for finding duplications from a whole genome in FASTA format? Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the ...
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34 views

Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
4
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2answers
85 views

Do any computational phylogenetic methods enable the specification of ancestral states?

Various phylogenetic algorithms estimate ancestral states of a phylogenetic dataset. Is there a way in either maximum parsimony, distance-based methods, or Bayesian inference to indicate what the ...
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2answers
66 views

Why does `pratchet()` in `phangorn` not find the most parsimonious trees?

I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the ...
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20 views

XCMS isn't evaluating the proper peak due to retention time drift

I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't ...
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3answers
1k views

visualisation of genome alignment

I was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and ...
6
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1answer
78 views

How to efficiently compute the exact percentage of non-unique k-mers in a genome for given k?

I'm looking for some software that can "efficiently" (time and memory) compute the exact percentage of non-unique k-mers in a genome for given k. I don't need the k-mers or the abundances itself, I ...
2
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1answer
375 views

gffread: GFaSeqGet errors on coordinate overhang

Disclaimer: I had this issue posted on Tuxedo Tools users group and shared it on Twitter, but could not get an answer to this from the developers, nor find documentation of this issue online. So, I'll ...
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2answers
177 views

Exon-exon junctions: compare experimental transcripts to reference annotation

My aim is to parse an experimental transcript set (obtained by RNAseq) to check which splice junctions are already reported in a reference annotation and which ones are new. I tried ...
2
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2answers
644 views

What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?

What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve? I am particularly interested in seeing the single nucleotide ...
5
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1answer
88 views

CRISPR Sequence Finder and Database Download

I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server. Are there other tools for finding ...
6
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2answers
215 views

Estimate the length of poly-A tails from randomly-primed RNAseq data

So a poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule. For my project, I would like ...
3
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0answers
38 views

Large range parameter identification

I have a model (ODE) of an enzymatic reaction, and I'd like to estimate four of its parameters to fit some available data. To obtain the model I am just using Mass-Action Kinetics. Some more details: ...
3
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1answer
447 views

problem of “ordering in physical positions” phasing SNPs with Shapeit

I'm trying to phase my data (whole genome resequencing SNPs) with Shapeit (from ped file) and I get this error message : ...
3
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1answer
316 views

Matlab scatter diagram

I have two columns of data, x and y, how can I make a ‘thermodynamic diagram’ with matlab? The z axis is the density value of dots, like below figure. The x-axis is angle, y-axis is distance. I want ...
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133 views

Chimera Alignments

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want ...
8
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2answers
84 views

How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY. I ...
5
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2answers
198 views

Software recommendation: find DNA sequence distribution over entire transcript

I would like to create a density/histogram of the distribution of a particular DNA sequence over the entire transcript using R and/or command line tools. From here, I would like to use the coordinates ...
6
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3answers
1k views

RIP-seq analysis?

Given an experiment consisting of an input (baseline RNA) and IP (pulldown to find RNAs bound to certain protein of interest)... Is a DE analysis performed over the RNA-seq data from the samples (lets ...
8
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4answers
96 views

Introduce errors in reference transcripts according to external dataset error model

I would like to modify some reference transcripts from Ensembl (D. melanogaster) to introduce a controlled rate of random errors in the sequences. The idea would be to introduce random base ...
5
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4answers
6k views

How to extract / convert gff3 CDS sequences to multifasta

I would like to extract all the CDS from a batch of genomes. I have found a perl script from BioStars but this does not seem to work for me. I would preferably like to have a script/ method which will ...
12
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2answers
2k views

How to convert fastq to fast5

fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract ...