Zerrin_data_March_2023 GLDS-37_RNAseq_Atha_Ler-0_GC

OSD_37 preliminary analysis with 1 sample.

The results of the analysis can be found in this folder.

Summary: Initial analysis performed on sample GLDS-37_rna_seq_Atha_Ler-0_sl-pool_GC_Rep5_R2-GC-C5_R1/2_trimmed.fastq).

Data/ Fastq files was pre-trimmed (See GeneLab pipeline for QC settings) data was downloaded from the OSDR.

For taxonomy quantitation

1.  Read QC (**FastQC**)

2.  Present QC for raw reads (**MultiQC**)

3.  Quality trimming (**Trim Galore!**)

4.  Create paired-end reads by combining single-end reads from two separate Fastq files (**FASTQ interlacer**)

5.  To identify bacteria and archaea (**MetaPhlAn**)

-Predicted taxon relative abundance omics levels

• Predicted taxon relative abundances

• Bowtie2 output

• SAM file

• BIOM file

• Predicted taxon relative abundances for KRONA

1.  Visualization (**Krona pie chart**)

For functional quantitation

1.  HuMAnN (it continues...)

MetaPhlAn performs taxonomic assignments with NCBI.

Here's the species abundance table/

species	species_id	abundance
Ralstonia pickettii	329	73.00088
Herbaspirillum huttiense	863372	16.31611
Pseudomonas fluorescens	294	6.973
Curvibacter gracilis	230310	1.96584
Neisseria subflava	28449	0.75498

Quick bar plot made using "https://julius.ai/"

import pandas as pd

# Load the species.tabular file
df = pd.read_csv('species.tabular', sep='\	')

# Display the first few rows of the dataframe
print(df.head())

import matplotlib.pyplot as plt

# Create a bar plot
plt.figure(facecolor='white')
plt.bar(df['species'], df['abundance'])
plt.xlabel('Species')
plt.ylabel('Abundance')
plt.title('Abundance of Species')
plt.xticks(rotation=90)
plt.tight_layout()
plt.show()

Species_abundance_Ler_test_sample

Microbial Species	Description	Habitat	Known Uses	Potential Applications	References
Ralstonia pickettii	Gram-negative, rod-shaped bacterium	Soil and water	Can degrade pollutants like toluene and chlorinated solvents [1]	Bioremediation of contaminated environments	NCBI: link
Herbaspirillum huttiense	Gram-negative, motile bacterium	Root systems of plants	Promotes plant growth by fixing nitrogen [2]	Biofertilizers to improve crop yields	NCBI: link
Pseudomonas fluorescens	Gram-negative, rod-shaped bacterium	Widespread in soil and water	Produces various beneficial compounds including antibiotics [3]	Biological pest control, disease suppression in plants	NCBI: link
Curvibacter gracilis	Gram-negative, curved rod-shaped bacterium	Soil and water	Degrades organic matter and plays a role in nutrient cycling [4]	Improvement of soil health and fertility	PubMed: link
Neisseria subflava	Gram-negative, coccus-shaped bacterium	Part of human commensal flora, found in the upper respiratory tract	Can be opportunistic pathogens but also contribute to the immune system [5]	Research on human health and diseases	NCBI Bookshelf: link