Learning Trail

This is a log of tools and small skills I am learning on the fly or deliberately during research in UCR …


  • January
  • February


  • September

    1. UNIX: Using a remote computer by ssh
    2. UNIX: How to use tmux
    3. RNASeq: Using FastQC and Trimmomattic
    4. RNASeq: Using STAR for mapping reads, aligner
    5. RNASeq: Bamtools to process SAM and BAM file
    6. RNASeq: IGV for visualizing genome
  • October

    1. UNIX: Writing bash scripts to automate command-line programs
    2. RNASeq: HTSeq for counting number of reads per genes
    3. RNASeq: Differential expression analysis using DESeq2 in R
    4. RNASeq: Using plasmodb for gene ontolgy (GO) analysis
    5. RNASeq: Heatmap visualization on DESeq2 data in R
  • November

    1. RNASeq: Using RSubread to count number of reads per genes
    2. RNASeq: Incorporating RSubread count file in DESeq2 in R
    3. RNASeq: Using Bed tools to count reads per gene
    4. RNASeq: How to do FPKM normalization by hand
  • ┬áDecember: I went to visit Bangladesh!