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Let's see how that works by using a small FASTQ file (~/data/fastq/small.fz) that contains NGS read data where each sequence is represented by 4 lines.
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cd ~/data/fastq # change into your ~/data/fastq directory# copy a small.fq file into a new ~/gzips directory mkdir -p ~/gzips cp -p /stor/work/CCBB_Workshops_1/misc_data/fastq/small.fq ~/gzips/ cd ~/gzips ls -lh small.fq # small.fq is 66K (~66,000) bytes long wc -l small.fq # small.fq is 1000 lines long |
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cd ~/data/fastqgzips # change into your ~/data/fastqgzips directory ls small.fq # make sure you have an uncompressed "small.fq" file gzip -c small.fq > sm2.fq.gz # compress the "small.fq" into a new file called "sm2.fq.gz" gunzip -c sm2.fq.gz > sm3.fq # decompress "sm2.fq.gz" into a new "sm3.fq" file |
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cd ~/data/fastqgzips # change into your ~/data/fastqgzips directory ls small.fq # make sure you have an uncompressed "small.fq" file cat small.fq | gzip > small.fq.gz |
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cd # make sure you're in your Home directory cat jabberwocky.txt | gzip > jabber.gz # make a compressed copy of the "jabberwocky.txt" file less jabber.gz # use 'less' to view the compressed "jabber.gz" file (q to exit) zcat jabber.gz | wc -l # count lines in the compressed "jabber.gz" file zcat jabber.gz | tail -4 # view the last 4 lines of the "jabber.gz" file zcat jabber.gz | cat -n # view "jabber.gz" text with line numbers (no zcat -n option) zcat jabber.gz | cat -n | tail +6 | head -4 # display lines 6 - 9 of "jabber.gz" text |
Exercise
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2-
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2
Display lines 6 - 9 of the compressed "jabber.gz" text
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