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Code Block

language	bash
title	Look at GFF annotation entries with less

mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools 
cp $CORENGS/yeast_rnarnaseq/sacCer_sacCer3.R64-1-1_20110208.gff . 
cp $CORENGS/yeast_rna/yeast_mrna.sort.filt.bam* .

# Use the less pager to look at multiple lines
less sacCer_sacCer3.R64-1-1_20110208.gff

# Look at just the most-important Tab-separated columns
cat sacCer_sacCer3.R64-1-1_20110208.gff | grep -v '#' | cut -f 1,3-5 | head -20

# Include the ugly 9th column where attributes are stored
cat sacCer_sacCer3.R64-1-1_20110208.gff | grep -v '#' | cut -f 1,3,9 | head

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Expand

title	Setup (if needed)

Code Block

language	bash

mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/sacCer_sacCer3.R64-1-1_20110208.gff .

Code Block

language	bash
title	Create a histogram of all the feature types in a GFF

cd $SCRATCH/core_ngs/bedtools
cat sacCer_sacCer3.R64-1-1_20110208.gff | grep -v '^#' | cut -f 3 | \
  sort | uniq -c | sort -k1,1nr | more

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Code Block

title	Filter GFF gene feature with awk

cat sacCer_sacCer3.R64-1-1_20110208.gff | grep -v '#' | \
  awk 'BEGIN{FS=OFS="\t"}{ if($3=="gene"){print} }' \
  > sc_genes.gff
wc -l sc_genes.gff

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