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how to calculate the number of chromosomes in the human annotation GTF file using Linux command?

I am trying to check the GTF annotation file for human, and I found that in first column which is the chromosome names just 1,2,........X,Y without chr so since the file is big I want to know how can I calculate the number of each chromosome (I mean how many 1, and how many2 ,..........etc). Is there any Linux command to do that. BTW I used the command

cut -f 1 .gtf_file > test

to cut the first column and save it in test file.

rna-seq
• 6,977 views • link
updated by Ram Ram • written by Y Tb Y Tb

look at the sort and uniq command. You may also find grep useful, specially the -v option that you can use to remove headers and comment lines.

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

2 answers

cut -f 1 foo.gtf | sort | uniq -c

I should note that this will tell you how many records there are in total for each chromosome or contig. If you instead wanted to know how many genes then it'd take a more involved script.

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written by Devon Ryan Devon Ryan 
awk '{print $1}' foo.gtf | sort | uniq -c

The first answer is correct, but I thought I'd share another, it just uses awk instead.

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updated by Ram Ram • written by Jason Jason

+1 from me too. awk is one of those indispensable tools that everyone that does file processing should know at least a little about.

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written by Devon Ryan Devon Ryan

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