[kevshaw@451]$ history
     1  w
     2  cat /usr/local/bin/pscr-bgal | less
     3  wget http://files.docking.org/99/20/27/170992027.mol2
     4  wget http://files.docking.org/files/99/20/27/170992027.mol2
     5  wget http://files.docking.org/protomers/99/20/27/170992027.mol2.gz
     6  gzip -dv 170992027.mol2.gz
     7  less
     8  less 170992027.mol2
     9  rm 170992027.mol2
    10  mkdir seq
    11  cd seq/
    12  wget ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
    13  gzip -dv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
    14  ls -al
    15  less Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa
    16  mv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa yeast.fa
    17  ls -al
    18  grep '^>' yeast.fa
    19  less yeast.fa
    20  ls
    21  samtools faidx yeast.fa
    22  ls
    23  less yeast.fa.fai
    24  bwa index yeast.fa
    25  ls -al
    26  less yeast.fa.bwt
    27  less yeast.fa.ann
    28  less yeast.fa.sa
    29  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_1.fastq.gz
    30  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_2.fastq.gz
    31  ls *.gz
    32  gzip -dv *.gz
    33  ls -al *.gz
    34  ls -al *.fastq
    35  less SRR507778_1.fastq
    36  head -20000 SRR507778_1.fastq > 1.fastq
    37  cat 1.fastq | wc -l
    38  head -20000 SRR507778_2.fastq > 2.fastq
    39  ls
    40  rm S*
    41  ls
    42  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    43  less yeast.sam
    44  less yeast.sam
    45  samtools sort -O BAM -T -I 0 -o yeast.bam yeast.sam
    46  samtools sort -O BAM -T -I O -o yeast.bam yeast.sam
    47  samtools sort -O BAM -T . -I 0 -o yeast.bam yeast.sam
    48  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    49  ls
    50  less yeast.bam
    51  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    52  samtools view yeast.cram | less
    53  samtools mpileup -f yeast.fa yeast.cram | less
    54  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    55  ls -al
    56  gzip -d snps.vcf.gz
    57  ls
    58  ls -al
    59  less snps.vcf
    60  cd
[kevshaw@451]$