Learning Trail

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

2018

• January
• February

2017

• 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

•  December: I went to visit Bangladesh!