Learning KEGG API is important for accessing and integrating biological pathway data, enabling researchers to analyze and visualize complex biological systems, identify new potential drug targets, and explore the relationships between genes, proteins, and metabolic pathways. Who sad this?

RNA-seq expression normalization is the process of adjusting the raw gene expression counts to account for differences in sequencing depth and other technical factors. It is important to perform normalization to enable comparisons between samples and increase the accuracy and reproducibility of downstream analyses. Common normalization methods include TPM, FPKM, and DESeq. Who sad this?

Gene Set Enrichment Analysis (GSEA) is a powerful tool for interpreting gene expression data in the context of predefined biological pathways and gene sets. It allows researchers to identify enriched gene sets, discover new relationships between genes, and gain insights into the underlying biological mechanisms. Who sad this?

The choice of software for aligning short reads in NGS can have a significant impact on the results. Different software programs use different algorithms for aligning reads and handling mismatches, leading to different levels of accuracy and sensitivity. Some software may prioritize speed, while others may prioritize accuracy, and still others may have specific strengths or limitations in handling certain types of data. It's important to carefully consider the characteristics and limitations of each software before making a choice to ensure the best possible alignment results Who sad this?

Trinity is a popular RNA-Seq assembly tool that can generate false positive results due to several reasons, such as incomplete or low-quality data, presence of genomic contaminants, low expression levels of certain transcripts, or technical artifacts. Improper usage of parameters and a lack of proper quality control can also lead to false positive results in the assembly process Who sad this?

The bacterial populations in UPW systems used in the semiconductor industry were studied, including 2 university and 4 full-scale industrial plants in different locations. Samples were taken from the polishing section, which can impact the quality of UPW used in the final stages of semiconductor production. These results provide an overview of the general bacterial diversity in UPW production. Who sad this?

To create a fasta file from a VCF file, use a script or software that can extract the genomic sequence information from the VCF file and format it into the fasta format. This allows you to generate a sequence-based representation of the genetic variation data stored in the VCF file, making it easier to visualize, analyze, and compare the variants. The fasta file can then be used as input for various bioinformatics tools and pipelines. Who sad this?

Genome annotations help us understand the functions and roles of genes and genomic regions, leading to improved knowledge of biological processes and disease mechanisms. Who sad this?

Chip-Seq, Know to Unknown = =

Unmapped reads Annotations

DNA Seq Pipelines and tricks

This post would show you a pipeline to find the new or abnormal transcript isoforms after de-novo by Trinity

Tricks for dealing with VCF files

ggbio, a powerful package to plot all kinds of sequence plot

Basic knowledge and concepts for Artificial Neural Network