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One of the first things you want to know about your annotation file is what gene features it contains. Here's how to find that: (Read more about what's going on here at Piping a histogram.)
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cd $SCRATCH/core_ngs/bedtools cat sacCer_R64-1-1_20110208.gff | grep -v '^#' | cut -f 3 | sort | uniq -c | sort -k1,1nr | more |
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Finally, the 8 re-ordered attributes are:
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1. chrom 2. start 3. end 4. ID 5. length 6. strand 7. gene 8. orf_classification |
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