GTF: Annotation and analyis of next generation sequencing (NGS) data
Bhagirathi Dash
December 2, 2018
GTF (Gene Transfer Format) Documentation
Here are documentations for GTF: GTF2.2 and gtf2.2.
One example:
GTFsnippet
Another example:
GTFsnippet
Data extraction from the GTF file
number of genes in the file
cat Xxxxxx.gtf|cut -f9|cut -d “;” -f2|sort -u |wc -l
cut –f9 Xxxxxx.gtf | cut –d ‘ ‘ –f2 | sort –u | wc –l
number of transcripts in the file
cat Xxxxxx.gtf|cut -f9|cut -d “;” -f1,2|uniq|cut -d “;” -f1|uniq -c |awk ‘$1==“1”’|wc -l
cut –f9 Xxxxxx.gtf | cut –d ‘ ‘ –f4 | sort –u | wc –l
number of single transcript genes
cat Xxxxxx.gtf|cut -f9 |cut -d “;” -f1,2 | uniq | cut -d “;” -f1 | uniq -c | awk ‘$1 == 1’ | wc -l
number of single-exon transcripts
cut –f9 Xxxxxx.gtf | cut –d ‘ ‘ –f2,4 | sort –u | cut –d ‘‘ –f1 | sort | uniq –c | grep –c “ 1 “
number of multi-exon transcripts
cut –f9 Xxxxxx.gtf | cut –d ‘ ‘ –f4 | sort | uniq –c | grep –c “ 2 “
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