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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Are there packages that can infer a sample's aneuploid cell proportion using sequencing data?
I have low-coverage WGS data from embryonic tissue (4-6 cells taken from early embryonic tissue). The exact number of cells is unknown and there's no strong prior on the aneuploid fraction, but I don'...
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Where to obtain fastq_illumina_filter
I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down.
Is there ...
- 412
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Variation in 16S rRNA between assemblers - how do I know which is real?
I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So ...
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Bioprocess data visualisation and analysis
I'm looking for some kind of software, ideally FOSS, that will allow us to plot, compare, annotate and add additional points to time series data from bioprocessing runs (bioreactors).
Many of the ...
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135
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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 ...
2
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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 ...
- 1,007
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91
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Allele effects by parental-origin estimated from genotyping array data
We are dealing with relatively large family data (> 1,000 trios) with genotyping array data.
We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
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Recode bgen files against reference genome
I have a set of .bgen files split by chromosomes, including both SNPs and INDELS (named with both rsids and chr_pos_a1_a2). I know a large portion of them are encoded on the wrong strand, and I want ...
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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
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136
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Is there a software that allows to convert a jpeg graph into dataset?
I have a very old graph as a .jpeg picture that I would like to convert into a dataset to be able to operate with it using R/python.
I have no idea if it is even possible.
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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
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591
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How to de novo hybrid assemble with Pacbio CCS and Illumina PE reads
I would like to perform de novo genome assembly on a diploid microalgal strain.
I have two datasets:
PacBio CCS/HiFi reads, low coverage.
Illumina PE 2x150 (standard shotgun)
Does anybody have any ...
- 31
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576
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If I have data from a full genome sequence, how can I search for a known pathogenic variant of a known gene?
I have a CS background, but am a bioinformatics neophyte
I did a full genome sequence which provided me with ~100GB of files (SNP VCF, Indel VCF, BAM, Indel TBI, SNP TBI, BAM BAI, CNV VCF, CNV TBI, CV ...
- 101
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How to get a consensus sequence from a nanopore fastq files?
I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed).
I usually generate a consensus sequence with "...
2
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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'...
