Errata and updates for Chapter 7

[haruosuz]

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(Page 131)

i() { (head -n 2; tail -n 2) < "$1" | column -t}

should be

i() { (head -n 2; tail -n 2) < "$1" | column -t; }

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Page 150

$ tail -n +6 Mus_musculus.GRCm38.75_chr1.gtf | awk -F "\t" '{print NF; exit}'
16

should be

$ tail -n +6 Mus_musculus.GRCm38.75_chr1.gtf | awk -F "\t" '{print NF; exit}'
9

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(Page 152)

(e.g., 50% with -S 50%).

should be

(e.g., 50% with -S 50%).

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(Page 154)

uniq -d test.bed | wc -l had no output. uniq -d Mus_musculus.GRCm38.75_chr1.bed | wc -l printed 22925. Thus,

A file with duplicates, like the test.bed file, has multiple lines returned:

uniq -d test.bed | wc -l
22925

should be

A file with duplicates, like the Mus_musculus.GRCm38.75_chr1.bed file, has multiple lines returned:

uniq -d Mus_musculus.GRCm38.75_chr1.bed | wc -l
22925

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(Page 156)

join -1 1 -2 1 -a 1 example_sorted.bed example_lengths_alt.txt # GNU join only

worked on Mac OS X 10.9.5

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(Page 163)

brew tap homebrew/science; brew install bioawk

should be

brew tap brewsci/bio; brew install bioawk

https://github.com/Homebrew/homebrew-science/issues/6617

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(Page 163)

(just as regular Awk sets the columns of a tabular text file to $1, $1, $2, etc.).

should be

(just as regular Awk sets the columns of a tabular text file to $1, $2, $3, etc.).

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(Page 163)

let’s read in example.bed

should be

let’s read in Mus_musculus.GRCm38.75_chr1.gtf

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(Page 164)

$ bioawk -c fastx '{print $name,length($seq)}' \
    Mus_musculus.GRCm38.75.dna_rm.toplevel.fa.gz > mm_genome.txt
$ head -n 4 mm_genome.txt

The file "Mus_musculus.GRCm38.75.dna_rm.toplevel.fa.gz" is located in not "chapter-07-unix-data-tools" but in "chapter-09-working-with-range-data" in the GitHub repository.

$ bioawk -c fastx '{print $name,length($seq)}' \
    ../chapter-09-working-with-range-data/Mus_musculus.GRCm38.75.dna_rm.toplevel_chr1.fa.gz > mm_genome.txt
$ head -n 4 mm_genome.txt
1	195471971
$cat mm_genome.txt 
1	195471971

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