Installation: https://docs.anaconda.com/anaconda/install/linux/
Managing environments: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
Creating a conda environment: conda create --name env_name
Creating a conda environment with a specific python version: conda create -n env_name python=3.6
Activating conda environment: conda activate env_name
Deactivating conda environment: conda deactivate
List conda environments: conda env list
List installed packages inside the conda environment: conda list
Installation from https://anaconda.org/bioconda/blast : conda install -c bioconda blast
Documentation : https://www.ncbi.nlm.nih.gov/books/NBK279690/
Performing blast:
Step 1: Creating a database locally - makeblastdb -in reference_sequences.fasta -out your_database_name -dbtype nucl -parse_seqids
replace nucl to prot to create database with amino acid sequences
Step 2: Performing blast - blastn -query query.fasta -db your_database_name -out blast_result_file_name.out -outfmt 6
replace blastn to blastp to perfomr protein blast
Links to understand blast output:
https://www.biostars.org/p/88944/
http://www.metagenomics.wiki/tools/blast/blastn-output-format-6
Installation from https://anaconda.org/bioconda/sra-tools: conda install -c bioconda sra-tools
Documentation: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
fasterq-dump : https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump \
Commands:
wget paste_hyperlink_here
fastq-dump SRRXXXXXX
fastq-dump -I --split-files SRRXXXXXX - for paired end data
fasterq-dump SRRXXXXXX
fasterq-dump -I --split-files SRRXXXXXX - for paired end data \
Installation from https://anaconda.org/bioconda/fastqc : conda install -c bioconda fastqc
Tool websource : https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Mannual: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
Video Tutorial: https://www.youtube.com/watch?v=bz93ReOv87Y&ab_channel=BabrahamBioinf
Command:
fastqc file_name.fastq
Installation from https://anaconda.org/bioconda/multiqc : conda install -c bioconda multiqc
Tool websource : https://multiqc.info/
Documentation: https://multiqc.info/docs/
Command: multiqc .
Installation from https://anaconda.org/bioconda/fastp: conda install -c bioconda fastp
Documentation: https://academic.oup.com/bioinformatics/article/34/17/i884/5093234
GitHub page: https://github.com/OpenGene/fastp
fastp video tutorial : https://www.youtube.com/watch?v=VrIW4EcHly4&ab_channel=MakeTheBrainHappy-ScientificExploration
Basic commands:
Single end: fastp -i read.fq -o out.fq
Paired end: fastp --in1 read1.fq --in2 read2.fq
Installation from https://anaconda.org/bioconda/qualimap : conda install -c bioconda qualimap
Tool websource: http://qualimap.conesalab.org/
Mannual: http://qualimap.conesalab.org/doc_html/index.html
Command:
./qualimap bamqc -bam bam_file.bam -gff gene_annotation.bed -outdir qualimap_results -outformat pdf \