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| cat yeast_mrna_gene_counts.bed | awk '
BEGIN{FS="\t";sum=0;tot=0}
{if($9 > 0) { sum = sum + $9; tot = tot + 1 }}
END{print sum,"overlapping reads in",tot,"records"}' |
There are 1144990 overlapping reads in 6235 records |
In Recall that in the yeast annotations from SGD there are 3 gene classifications: Verified, Uncharacterized and Dubious, and the Dubious ones have no experimental evidence so are generally excluded.
Exercise: What is the total count of reads mapping to gene features other than Dubious?
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The classification is in the 7th column of sc_genes.bed. Use cut to isolate that field, sort to sort the resulting values into blocks, then uniq -c to count the members of each block. |
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| grep -v 'Dubious' yeast_mrna_gene_counts.bed | awk '
BEGIN{FS="\t";sum=0;tot=0}
{if($9 > 0) { sum = sum + $9; tot = tot + 1 }}
END{print sum,"overlapping reads in",tot,"records"}' |
There are 1093140 overlapping reads in 5578 records |
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