VCF to GENEPOP FORMAT
Hi people :3
I'm searching to see if there is a program to transform VCF files to genepop format (.gen). Anyone knows a program or maybe have a script to do this?
Thanks for your time :3
Adapter trimming in 10x Data and CellRanger Make Counts Expected Cells
Adapter trimming in 10x Data and CellRanger Make Counts Expected Cells
I am working with 10x data for scRNA seq and I have encountered an issue while using Cellranger count after performing trimming of poly(A) tails and low-quality reads. I specifically trimmed the low-quality reads and poly(A) tails in the R2 reads using Cutadapt. During the Cellranger count step, I received an error message ...
Methods to filter data for constructing a gene network
Methods to filter data for constructing a gene network
Hello guys!
I have a matrix with gene expression counts (rows -> genes, columns -> samples). I have applied the Pearson correlation to these data because I want to generate an adjacency matrix. My purpose is to apply graph based methods on the network that it will be constructed.
My main problem is that the adjacency matr...
How to select differential abundant ASVs/ Keggs from ancombc2 for enrichment analysis
How to select differential abundant ASVs/ Keggs from ancombc2 for enrichment analysis
Hello all,
I have been working on my 16S amplcon data for a while now and I have gotten to the last of the downstream analysis where I am stuck and I dont know hwo to move forward. I have data set that I woud say loks like a full factorial; Genotype (4 levels; G1, G2, G3, & G4), Day (3 levels; D1, D2 & D3), Treatment (6 lev...
Top 10 most useful (to me) commands when working with FASTA files
Top 10 most useful (to me) commands when working with FASTA files
Working with FASTA files is a daily task for many biologists and has been a daily task of mine for a few years now. I wrote this quick post to just provide some examples on how to manipulate FASTAs using SeqKit.
Due to the advent of next-gen sequencing, humanity has amassed petabases of data and it appears that bioinformat...
Is your UMAP lying to you?
Is your UMAP lying to you?
Intro: to see is to know
Humans are very visual creatures, and the way we experience science - especially biological science - is predominantly through visualizations. From beautiful immunofluorescence stainings to western blot bands, going through action potential recordings, scientists look at data before anything else....
Decoding Metabarcoding: A Look at Data Processing Software Suites and Pipelines (part2)
Decoding Metabarcoding: A Look at Data Processing Software Suites and Pipelines (part2)
Navigating Through Sequencing Platforms
Navigating the ever-changing world of metabarcoding feels a bit like trying to keep up with the latest smartphone tech—it's a constant race. The sequencing platform you choose is becoming more and more crucial. Second-generation technologies, like Illumina, are popular hotshots in hi...
Decoding Metabarcoding: A Look at Data Processing Software Suites and Pipelines (part1)
Decoding Metabarcoding: A Look at Data Processing Software Suites and Pipelines (part1)
In the ever-evolving world of bioinformatics, researchers continually seek new tools to process and analyze metabarcoding data. Two primary categories of software have emerged to cater to these needs: suites hosting multiple algorithms and pre-defined pipelines. This series of blog posts delves into the strengths and limita...
Genomics in R, Part 3: Gene Calling and Annotation
Genomics in R, Part 3: Gene Calling and Annotation
Suppose you've sent out some strains/samples/whatever for sequencing, and you've just received a fresh dump of sequencing data files. How do you go about finding what's in that sequence? Where do the genes start and end? How do we take a string of nucleotides/amino acids and convert it to real gene names like rpoB or BRCA1?...
Genomics in R, Part 2: Phylogenetic Reconstruction
Genomics in R, Part 2: Phylogenetic Reconstruction
My last post covered getting started with R and using the DECIPHER package for visualizing and aligning sequences. In this post, I'd like to cover a really popular topic in genomics: phylogenetic reconstruction.
What Is Phylogenetic Reconstruction?
Evolutionary biologists are very interested in charting the evolutionary h...