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SQL-SRA-QRY-unjoined-anno-counts-by-type.txt
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SQL-SRA-QRY-unjoined-anno-counts-by-type.txt
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select 'table: study';
select 'total records', count(*) from study;
-- study_description
select 'study:study_description', 'fragmentation_annotation', sum(c)
from
(
select count(*) as c from study where
study_description like "% shear%"
or study_description like "% restriction%"
or study_description like "% digest%"
or study_description like "% fragment%"
or study_description like "% breaks %"
or study_description like "% nebulis%" or study_description like "% nebuliz%"
or study_description like "% acoustic%"
or study_description like "% sonic%"
);
select 'study:study_description', 'adapter-ligation_annotation', sum(c)
from
(
select count(*) as c from study where
study_description like "% adapter%"
or study_description like "% ligat%"
or study_description like "% blunt%"
or study_description like "% phosphorylat%"
or study_description like "% overhang"
or study_description like "% t4-PNK"
or study_description like "% t4"
or study_description like "% pnk"
or study_description like "% kinase"
);
select 'table: experiment';
select 'total records', count(*) from experiment;
-- library_construction_protocol
select 'experiment:library_construction_protocol', 'fragmentation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%" or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
);
select 'experiment:library_construction_protocol', 'adapter-ligation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
);
select 'experiment:library_construction_protocol', 'fragmentation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
);
-- library_selection
select 'experiment:library_selection', 'fragmentation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_selection like "% shear%"
or library_selection like "% restriction%"
or library_selection like "% digest%"
or library_selection like "% fragment%"
or library_selection like "% breaks %"
or library_selection like "% nebulis%" or library_selection like "% nebuliz%"
or library_selection like "% acoustic%"
or library_selection like "% sonic%"
);
select 'experiment:library_selection', 'adapter-ligation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_selection like "% adapter%"
or library_selection like "% ligat%"
or library_selection like "% blunt%"
or library_selection like "% phosphorylat%"
or library_selection like "% overhang"
or library_selection like "% t4-PNK"
or library_selection like "% t4"
or library_selection like "% pnk"
or library_selection like "% kinase"
);
select 'experiment:library_selection', 'fragmentation_anno', sum(c)
from
(
select count(*) as c from experiment where
library_selection like "% clone%"
or library_selection like "% clonin%"
or library_selection like "% pcr %"
or library_selection like "% amplif%"
or library_selection like "% polymerase%"
or library_selection like "% taq%"
or library_selection like "% phusion%"
or library_selection like "% temperat%"
or library_selection like "% thermal%"
or library_selection like "% anneal%"
or library_selection like "% denature%"
);