Microbiome metagenomics analysis of Kilifi creek mangrove sediments

[kipkurui]

Briefly comment on this issue why you'd be interested in this project.

[shabanimziray]

I am interested in this topic because it will complement my current PhD project which is about Metagenomics. I might apply the pipelines and tools generated in this project to address the voluminous metagenomic data that are anticipated to be generated in my project

[elizabeth5127]

i have a passion on metagenomics that get i better understanding on the pipeline and tools involved in data analysis

[bwanya]

I’m interested in this project too as my second choice

[Stanslauskiilu]

I interested in this mini project as my first option

[tolbertsonda]

I will be happy to join the team working on this project

[kipkurui]

@karegapauline, you are part of this project...comment on this issue so that I can assign you

[tolbertsonda]

Project #2 will enable me learn how these microbiome/metagenomics pipelines are developed and work

[karegapauline]

I am interested in this project as it will enable me to understand more on genomic aspects that I need.

[henrick-aduda]

bash script for running trimmomatic on hpc

!/bin/bash

SBATCH -p batch

SBATCH -w compute05

SBATCH -J trimming

SBATCH -n 2

SBATCH -o out.txt

SBATCH -e slurm_errors

module load trimmomatic

module load trimmomatic/0.38

changing directory to our working directory(data directory)

cd /home/user11/group5_miniproject

picking each read in the samples folder using a for loop

for infile in *1.fastq.gz do base=$(basename ${infile} 1.fastq.gz) java -jar /export/apps/trimmomatic/0.38/trimmomatic-0.38.jar PE ${infile} ${base}2.fastq.gz \ ${base}_1.trim.fastq.gz ${base}_1un.trim.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz HEADCROP:7 done