Unix History

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cutcut, capture the outputcut, pipe the output to grepExamine a marker, translating the output
s_1_sequence.txt.gzlsgunzipmanmorecatwcheadcutgrepsortuniq>|1. Decompress the file2. Count the number of raw reads (250,000)3. Count the number of reads with barcode CGATA (19,501)4. Capture all FASTQ records for ACCAT into a file calledsample_01.fq (you should get 18352 records, 73408 lines)5. Determine the count of all barcodes in the file286 CTAGT7900 TCAGA10659 ACTGC10931 TGACC11536 GAGAT11871 CTGAA14409 CGGCG14508 TGGTT18226 GAAGC18352 ACCAT18375 TCGAG19501 CGATA23012 AATTT26336 GCATT31136 CTAGG1. Use head when building a command, cat once the command is working2. Look at the -n option for the head command, the -l option for wc3. The “^” character means “must occur at beginning of line” in a grep search4. Look at the grep options: -c, -v, -A, -B5. Read the man pages for sort and uniq to learn how to combine them
Page 1 and 2: Unix HistoryUnicsUnixTSS1 to 4UnixT
Page 3 and 4: What computers can run Unix?•Appl
Page 5 and 6: The Terminal WindowMake it comforta
Page 7 and 8: In UNIX everything is a file organi
Page 10: Create a series of directories
Page 13 and 14: Absolute and relative pathsHow do I
Page 15 and 16: Paths/roothome usr bin ...cresko ca
Page 17 and 18: Relative Path/roothome usr bin ...c
Page 19 and 20: Special files -- ‘dot’/.root. .
Page 21 and 22: Special files -- ‘dot dot’/..ro
Page 23 and 24: Absolute and relative pathsSpecial
Page 25 and 26: Binary programs - ls, cp, mkdir, et
Page 27 and 28: Relative and absolute paths/home/ub
Page 29 and 30: Relative and absolute paths/home/ub
Page 31 and 32: Are you typing? You’re doing it w
Page 33 and 34: Three variants to lsls -l ls -la ls
Page 35 and 36: 1. Move to the directory /etc• Wh
Page 37 and 38: What is a tar archive?tar = tape ar
Page 39 and 40: The FASTQ File FormatFASTA>HWI-ST07
Page 41 and 42: The FASTQ File Format, ctd@HWI-ST07
Page 43 and 44: The FASTQ File Format, ctd@HWI-ST07
Page 45 and 46: Count raw reads:Count reads with ba
Page 47 and 48: The Shell’s Killer App: Pipes, ct
Page 49 and 50: The Shell’s Killer App: Pipes, ct
Page 51: The Shell’s Killer App: Pipes, ct
Page 55: Count raw reads:wc -l s_1_sequence.

Unix History

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