• Take your favorite protein and find associations using various databases, viz. Genecrads, String, Genemania, IntAct, MINT et.c and reach consensus on the type of interactions your protein of interets makes.
• Can you list a few visualizers and import your network to them?
1. Data validation from integrated sources
2. Protein-Protein interaction assay(pull down),in vivo
3. Protein localization studies in silico
4. Cleavage sites,if any
5. A simple query from STRING, EMBL/Gene cards/iHOP
• Can we accommodate information relevant to different stages of development/cell cycle in protein interaction maps?
• List any two next generation sequencing platforms and their applications
• What is a sequencing chemistry? Explain the difference between single end reads and paired end reads

Prelude:

• Download the repositories from various sources, viz. GEO, Repositive and other genebanks
• FTPing the references
• Compare the paired-end, mate-pair and single-end reads
• making batch scripts for next generation sequencing
• Overview of all NGS tools, viz. Checking quality mappable reads using Fastqc, Variant calling using vt and varscan, GATK and online tools
• Overview of Galaxy, Git and bitbucket/Atlassian

Example with Exome sequening data

Using the Server

All users by default are logged into their respective user accounts, viz. Test1, test2, test3 and test4
To login, open the terminal and first ssh 192.168.1.18, please enter username test1/test2/test3/test4 (password shall be informed to you later)
Once login, You will be at
/home/test1
Please use your working directory as /home/bioinfo
So to move to that folder, simply type cd ../bioinfo
All your programs/commands/scripts are available in that folder
Please refer sample batch script for exome sequencing here.

Example with Exome sequening data

#Indexing already done using bowtie2, BWA and samtools: ../data/hg38/
#All scripts and commands are to be run from /home/prash/share/analyses/Expipe
#fastqc already one for all samples. Pl check the folder out/
#../bowtie2-master/./bowtie2 -x ../data/hg38/hg38 -1
../../../../admin1/share/km/raw_data/sample_R1.fq.gz  -2
../../../../admin1/share/km/raw_data/sample_R2.fq.gz > sample.sam

#samtools import ../data/hg38/hg38.fa sample.sam sample.bam

#samtools sort sample.bam -o sample.sorted.bam

#samtools index sample.sorted.bam sample.sorted.bam.bai
#samtools merge sample.merged.bam sample.sorted.*
#samtools mpileup sample.sorted.bam -o sample.mpileup.bam


#java -jar varscan/varscan.jar mpileup2snp sample.mpileup.bam > sample.mpileup.snps

#java -jar varscan/varscan.jar mpileup2indel sample.mpileup.bam > sample.mpileup.indels

#java -jar ../varscan/varscan.jar filter sample.mpileup.snps >sample.mpileup.snps.filter

#java -jar ../varscan/varscan.jar readcounts sample.mpileup.bam >sample.mpileup.readcounts

#samtools mpileup -uf ../data/hg38/hg38.fa sample.sorted.bam
| bcftools view - > sample.var.raw.bcf
##bcftools view sample.var.raw.bcf | vcfutils.pl varFilter -D100 > sample.var.flt.vcf

#samtools calmd -Abr sample.sorted.bam ../data/hg38/hg38.fa > sample.baq.bam 

samtools mpileup -uf ../data/hg38/hg38.fa sample.sorted.bam | bcftools call -c -v -o sample.vcf.gz

#samtools mpileup -go sample.bcf -f ../data/hg38/hg38.fa sample.bam

#bcftools call -vmO z -o sample.vcf.gz sample.bcf

#Preparing VCF for querying and indexing using tabix:

#tabix -p vcf sample.vcf.gz

#preparing graphs and stats:

#bcftools stats -F ../data/hg38/hg38.fa -s sample.vcf.gz > sample.vcf.gz.stats
#Plots in directory plots

#plot-vcfstats -p plots/ sample.vcf.gz.stats

#Data Filtering:

#bcftools filter -O z -o sample_filtered.vcf.gz -s LOWQUAL -i'%QUAL>10' sample.vcf.gz