This repository for Workshop Course Homeworks in Bioinformatics Institute 2023-2024
For Project 9 CITE-seq was used to perform a comprehensive single-cell analysis of human bone marrow. Utilizing Scanpy, the study processed a dataset of 33,454 cells, identifying eight distinct cell groups. Focus was given to monocytes and myeloid dendritic cells, characterized by specific gene markers such as FCN1, VCAN, AIF1, SPI1, and CD68.
For Project 8 we delved into the intricacies of T-cell receptor β-chain repertoire diversity across CMV+ and CMV- donors. Utilizing RepSeq analysis, 16 TCRB samples were annotated.
For Project 7 we investigated the microbial communities in ancient dental calculus samples.
Pipeline using QIIME2 was applied to analyse 16s rRNA amplicon sequencing data.
The Standard database in Kraken2 was used for metagenomic profiling of Shotgun Sequencing data, and Pavian was used to visualise the results. The Tannerella forsythia genome was downloaded from the NCBI database using the entrez-direct package, and the bwa algorithm was used to index it and then align metagenomic contigs to it. The samtools was used to compress, sort and index the reads aligned to the reference. The bedtools was used to find intersections of the alignment with the genome annotation file.
For Project 6 we explored Saccharomyces cerevisiae transcriptome dynamics during a 30-minute anaerobic fermentation.
Used RNA-seq and HISAT2, featureCounts, DESeq2 for alignment, quantification, and differential expression analysis. Identified 1905 significant genes, revealing upregulation in glycerol biosynthesis and glucose transport. To determine the primary biological processes involving differentially expressed genes used goSlipMapper and ShinyGO
For Project 5 we performed genotyping and SNP annotation of human 23andMe project data.
During the project we analysed data from 23andMe test of our teacher in Bioinformatics. We used plink to convert the raw data to vcf format. Haplogroup identification was performed with mthap for mtDNA and Y-SNP Subclade Predictor + YSEQ Clade Finder for Y-chromosome. SNPs were annotated with SnpEff with Human Reference Genome build 37. To compare obtained data with the ClinVar database we used SnpSift. Further SNP analyses were carried out using SNPedia database.
For Project 4 we performed tardigrade Ramazzottius varieornatus genome annotation and protein function prediction.
During the project we used precomputed AUGUSTUS results, including fasta and GFF files to perform a structural annotation of Ramazzottius varieornatus (strain YOKOZUNA-1) genome. To localise proteins associated with DNA we performed a local alignment-based search with blastp. Subcellular localization predictions were made with WoLF PSORT and TargetP. To identify homologous sequences we used BLAST search against the UniProtKB/Swiss-Prot database. To identify protein domains and motifs in the selected protein sequences we performed pfam predictions with HMMERz and Pfam databases.
For Project 3 we did de novo assembly of its genome. Data is lost. Details to be disclosured soon.
For Project 2 we did variant calling of deep sequencing data (Influenza A virus (H3N2) hemagglutinin gene).
During the project we also used FastQC, Trimmomatic, bwa, samtools and VarScan, but this time we used Snakemake script to make automatisation. For data visualisation IGV was used
For Project 1 we did variant calling of Escherichia coli WGS.
During the project we did data preprocessing with FastQC and Trimmomatic, then we mapped trimmed reads to a large reference genome with bwa, generated mpileup file using samtools and performed variant calling with VarScan