weitinglin/201511coursera-command-line

practice

Course: Command Line For Genomic Data

201511-12##

Professor: Liliana Florea, PhD, John Hopskins University

• Unix commands
• Basic commands
• Pipes
• Sequences and genomic features
• Formats: Fastq, BED, GTF, SAM
• Tools: Samtools, Bedtools
• Alignment and sequence variation
• Bowtie, BWA
• Samtools, Bcftools
• Application: variant calling
• Transcriptomics
• Tophat
• Cufflinks
• IGV
• Application: RNA-seq analysis

#Week1: Basic Command Line

sort months sort -r months sort -k2 months sort -k 2n months sort -k 2nr months sort -k 3 months sort -k 3 -k 2n months cut -f1 months cut -f1-3 months cut -d '' -f1 months # d 辨識特定的符號做為分別 sort -u months uniq months uniq seasons | sort -u uniq -c grep root /.sample grep " 12 winter" months grep -n " 12 winter" months diff orchard orchard.1 comm -1 -2 orchard orchard.1 #Week2

#Week3

#Week4: RNA-seq