[kevshaw@451]$ history
     1  date
     2  ls
     3  cd blast
     4  ls
     5  less primers
     6  blastn -db human_genomic -word_size 7 -query primers -out tg.out
     7  cat primers
     8  less tg.out
     9  cd
    10  mkdir seq
    11  cd seq/
    12  ls
    13  wget http://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
    14  ls
    15  gzip -dv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
    16  ls
    17  less Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa
    18  grep '^>' Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa
    19  mv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa yeast.fa
    20  ls
    21  samtools faidx yeast.fa
    22  ls
    23  ls -l
    24  less yeast.fa.fai
    25  bwa index yeast.fa
    26  ls
    27  ls -l
    28  wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_1.fastq.gz
    29  wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_2.fastq.gz
    30  ls
    31  gzip -dv SRR507778_1.fastq.gz
    32  ls
    33  ls -l
    34  gzip -dv SRR507778_2.fastq.gz
    35  ls
    36  less SRR507778_1.fastq
    37  head -20000 SRR507778_1.fastq
    38  head -20000 SRR507778_1.fastq > 1.fastq
    39  head -20000 SRR507778_2.fastq > 2.fastq
    40  ls -l
    41  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    42  ls
    43  ls -l
    44  less yeast.sam
    45  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    46  ls
    47  less yeast.bam
    48  samtools view yeast.bam | less
    49  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    50  ls
    51  ls -l
    52  samtools mpileup -f yeast.fa yeast.cram | less
    53  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    54  ls
    55  gzip -dv snps.vcf.gz
    56  less snps.vcf
    57  cd
[kevshaw@451]$