Publications by Nguyen Ngoc Thieu
PROCESSING SEQUENCING DATA FASTQ WITH TRIMMOMATIC-0.39
Trimmomatic-0.39 is used to preprocess sequencing data fastq for pair-end reads (PE). Installing trimmomatic-0.39 Download Trimmomatic-0.39 from its website to ‘Downloads’ as ‘Trimmomacti-0.30/trimmoatic-0.39.jar’. Then I copy trimmomatic-0.39 to ‘/usr/local/bin’ in order to globally run trimmomactic-0.39. Run trimmomatic program from ...
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SEQUENCING DATA FASTQ QUALITY CHECK WITH FASTQC
Package needed for loading html file: {r echo=FALSE, results=‘asis’} library(shiny) includeHTML(“/Users/nnthieu/fastqs/SRR576933_Quality Check.html”) ## Warning: `includeHTML()` was provided a `path` that appears to be a complete HTML document. ## ✖ Path: /Users/nnthieu/fastqs/SRR576933_Quality Check.html ## ℹ Use `tags$iframe()` to inc...
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Microbial WGS Upstream Data Analysis
Data Data for analysis are downloaded from ftp.sra.ebi.ac.uk/vol1/fastq and data for reference is downloaded from NBCI. The genome is of Mycobacterium tuberculosis H37Rv, assession is SRR28714667. Codes below are runned in Linux: setwd("/Users/nnthieu/Rosalind/") # Genotype: CalA_resC6 system("wget -P ./raw/ ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/078...
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WGS Data Analysis
Data Data for analysis are downloaded from ftp.sra.ebi.ac.uk/vol1/fastq and data for reference is downloaded from NBCI. The genome is of Mycobacterium tuberculosis H37Rv, assession is SRR28714667. Codes below are runned in Linux: setwd("/Users/nnthieu/Rosalind/") # Genotype: CalA_resC6 system("wget -P ./raw/ ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/078...
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Rosalind’s Genome Data Analysis Exercises Using R - Part 1
setwd("/Users/nnthieu/Downloads/GenomeProject1000/Blast/") library(Biostrings) ## Loading required package: BiocGenerics ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:stats': ## ## IQR, mad, sd, var, xtabs ## The following objects are masked from 'package:base': ## ## anyDuplicated, aperm, appe...
507 sym R (11461 sym/39 pcs)
Analyzing .fatsq File Genome Data Using Linux Combinned with R
Download .fastq data from NBCI I get .fastq data from NBCI using coding as follow: Set working directory: setwd("/Users/nnthieu/Downloads/GenomeProject1000/Blast/") Firstly, create a “accession.txt” file containing fastq file on NBCI I need to download: ‘nano accession.txt’ SRR30352484 SRR30298594 SRR30298562 SRR722403 SRR30352543 SRR303525...
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Gene Alignment Blast
In this tutorial, I will perform translational genomics. I will take a gene from one genome and identify its location in another using Blast. Download data Here, I went to NCBI.nlm.nih.gov and searched for Seriola rivoliana then clicked on the Assembly link under Genomes. The download link can be found on the right hand side under Download the Gen...
1631 sym R (1204 sym/5 pcs) 1 img
PLINK for genomic data analysis
Install PLINK Download PLINK from its website to a local folder “plink_mac_20231211” then go to ‘Terminal’ and run commands as follow: cd ~/Downloads/plink_mac_20231211 – verify plink exist in the folder ls – move plink to /bin sudo mv plink /usr/local/bin/ cd /bin – verify plink exist in the folder “/usr/local/bin” ls – make t...
2127 sym R (5294 sym/17 pcs) 1 img
Assess The Immunogenicity of Investigated Vaccine GBP5 Compared To ChAdO
Investigated vaccine A Phase III Study to Assess the Immunogenicity and Safety of SARS-CoV-2 GBP5 in Adults Aged 18 Years and Older. Dose 1 at Visit 2, dose 2 at Visit 4. Test for immunogenocity at Visit 6, 2 weeks after the second dose. Data for this analysis is from Vietnamese subjects. Loading data library(tidyverse) ## ── Attaching core ti...
900 sym R (11735 sym/37 pcs) 1 img
HOSPITAL READMISSION PREDICTION USING PYTHON
HOSPITAL READMISSION PREDICTION USING PYTHON Using EHR data to build machine learning models to predict the likelihood that a patient could be readmitted to hospital within 30 days after discharging. This post aimed at showing how to process EHR data before building machine learning models. The readmission rate is an important KPI to measure the ...
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