Linux part II

Prerequisite:

Connect to server (ssh)
Basic Linux command and getting help (pwd, ls, ln, cd, cp, scp, mv, mkdir, rm, wget, git clone, du, df)

Download (wget, git clone) and Execute (decompress, install) program
- download and decompress ncbi-blast-2.9.0+-x64-linux.tar.gz (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST)
Read (cat, head, tail, more, less, wc, diff) and edit (touch, nano, vim) file
- git clone the repo for example file (https://github.com/enormandeau/ncbi_blast_tutorial.git)
- fasta format: 2 lines per sequence
  1. header
  2. sequence
- line counts (hint: using wc)
- vim tutorial: (hint: using vim command mode)
  1. change all reference_ to ref- in reference.fasta
  2. makeblastdb and blastn (practice with ln)
Advanced file edit (grep, cut, sed, awk, join, paste, sort, uniq)
- download test vcf file (wget https://goo.gl/z1TBu9 -O test.vcf)
- vcf format (at least 9 column)
- line counts of headers (hint: using wc and grep)
- awk, paste
- categories counts of col7 (hint: using cut, sort, uniq)
(optinal) Docker
- run a linux base container
- build your own docker image with interactive mode
- build your own docker image with Dockerfile
- run your docker image
- manage multi-images with docker-compose

Download and install samtools, then build index for reference.fasta
- report line counts of col1 = chr1 and col2 between 10000 ~ 20000 (including 10000 and 20000) and col3 != . in test.vcf (see Topics3), and write column 1, 2, 4, 5 to new.vcf
upload to server (ask shanghung in slack for more detail)