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.
76
questions
24
votes
4
answers
890
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Tools for simulating Oxford Nanopore reads
Are there any free open source software tools available for simulating Oxford Nanopore reads?
- 5,080
17
votes
7
answers
6k
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How to convert BED to GFF3
I would like to convert a BED format to GFF3.
The only useful tool that I could find via a google search seems to be Galaxy, ...
- 2,676
13
votes
8
answers
16k
views
Fast way to count number of reads and number of bases in a fastq file?
I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
- 10.1k
13
votes
2
answers
3k
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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 ...
- 2,676
10
votes
4
answers
4k
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How do I generate a color-coded tanglegram?
I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
- 955
9
votes
3
answers
4k
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How to convert GFF3 to GTF2
I would like to convert a file in gff3 format to a gtf2.2 format.
The reason why I would like to do this is: I have a set of ...
- 2,676
9
votes
1
answer
133
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 ...
- 258
9
votes
1
answer
233
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
votes
4
answers
105
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 ...
- 2,676
8
votes
2
answers
197
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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 ...
- 181
8
votes
2
answers
2k
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. ...
- 2,676
8
votes
2
answers
289
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 ...
- 517
7
votes
3
answers
231
views
Visualization tools for 3C/Hi-C long-range interaction data?
I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.
After viewing it in the UCSC genome browser, I have confirmed ...
- 397
7
votes
3
answers
2k
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 ...
- 2,676
7
votes
3
answers
2k
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 ...
- 405
7
votes
5
answers
605
views
What motif finding software is available for multiple sequences ~10Kb?
I have around ~3,000 short sequences of approximately ~10Kb long. What are the best ways to find the motifs among all of these sequences? Is there a certain software/method recommended?
There are ...
- 1,691
6
votes
3
answers
510
views
tools to reconcile experimental transcripts with reference annotation
Looking for tools to reconcile alignment file of experimental transcripts mapped to genome (SAM/BAM) with the reference transcriptome annotation (GTF) from Ensembl (organism: D. melanogaster).
The ...
- 2,676
6
votes
2
answers
317
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 ...
- 1,691
6
votes
2
answers
146
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 ...
- 4,703
6
votes
1
answer
105
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 ...
- 69
6
votes
2
answers
462
views
What tools can I use for a bacterial core/pan genome pipeline?
I want to perform a genome comparison on a group of isolates. I want to look into two broad groups of taxa and compare the accessory genome in each group. I have been using prokka (v1.12) and roary (...
- 955
5
votes
5
answers
9k
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 ...
- 955
5
votes
2
answers
842
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 (...
- 2,676
5
votes
2
answers
259
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 ...
- 161
5
votes
1
answer
137
views
How can I dock a protein to a nucleic acid?
I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.
What tool can I use?
- 53
5
votes
1
answer
127
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 ...
- 173
5
votes
0
answers
31
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 ...
- 645
4
votes
4
answers
788
views
Analysis of differential transcript usage (DTU)
Recent breakthroughs in bioinformatics tools for quantification (e.g.
Cufflinks/Kallisto/Salmon etc.) and tools which can identify differential transcript usage (DTU) (e.g. DRIMSeq, Cufflinks etc.) ...
4
votes
2
answers
427
views
Reordering scaffolds according to a reference without a genetic map
I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
- 325
4
votes
2
answers
289
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 ...
- 2,676
4
votes
1
answer
220
views
Software recommendations - DNA composition
I'm looking to generate data based on the DNA composition of a region of my genomes (data is incomplete genomes from HiSeq runs in fasta format). I'm looking for software which will give me sliding ...
- 955
4
votes
2
answers
738
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 ...
- 345
4
votes
1
answer
757
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). ...
- 3,161
4
votes
2
answers
90
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 ...
- 317
3
votes
1
answer
920
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 :
...
- 33
3
votes
1
answer
2k
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 ...
- 51
3
votes
1
answer
101
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 ...
- 3,130
3
votes
1
answer
131
views
Extract compounds/proteins from plant genomic data
I want a process by which I can identify genes within plant genomes; i.e. a process that works for all plants, not just for a single species.
I'm wondering, if, by bioinformatic means only, it is ...
3
votes
1
answer
140
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 ...
- 192
3
votes
1
answer
899
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 ...
- 2,676
3
votes
0
answers
43
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:
...
- 131
2
votes
3
answers
252
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 ...
- 2,459
2
votes
2
answers
317
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. ~...
- 697
2
votes
1
answer
116
views
Visualization of mutations in (part of) viral genome - existing tools?
I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info:
but for individual sequences, probably on the base of the vcf files generated by the ARTIC ...
- 216
2
votes
2
answers
1k
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 ...
- 2,459
2
votes
2
answers
448
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 ...
- 2,459
2
votes
1
answer
74
views
Is there a graphical/interactive 16S rRNA clustering method?
I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.
Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
- 909
2
votes
0
answers
43
views
How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?
How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files?
The way flow-jo exports is in wide rather than ...
- 131
2
votes
0
answers
60
views
Which GWGAS Tool is 'better', MAGMA or LDSC?
I am currently doing a project regarding gene-based analysis and gene-set analysis given a certain GWAS dataset, I only know 2 well known gene-based analysis tool which is LDSC and MAGMA.
As of now, I'...
2
votes
0
answers
343
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 ...
- 21