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Copy pathSQL-SRA-QRY-lib-cons-prot-venn.txt
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SQL-SRA-QRY-lib-cons-prot-venn.txt
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-- Previous results -- used for Venn diagram
-- Fragmentation: 2,860
-- Ligation: 2,028
-- Enrichment: 2,788
-- All: 1,409
-- Fragmentation+Ligation: 1,580 (a ∩ b)
-- Fragmentation+Enrichment: 1,857 (a ∩ c)
-- Ligation+Enrichment: 1,709 (a ∩ c)
-- Fragmentation+Ligation
select 'table: experiment, field: library_construction_protocol [fragmentation + ligation]';
select '(study-exp join)experiment:library_construction_protocol', 'fragmentation+ligation', count(*)
from
(
select
stu.study_accession id, count(library_construction_protocol) from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
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%"
) AND
(
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%"
or library_construction_protocol like "% a-tail%"
)
group by id
);
-- Fragmentation+Enrichment
select 'table: experiment, field: library_construction_protocol [fragmentation + enrichment]';
select '(study-exp join)experiment:library_construction_protocol', 'fragmentation+enrichment', count(*)
from
(
select
stu.study_accession id, count(library_construction_protocol) from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
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%"
)
AND
(
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%"
)
group by id
);
-- Ligation+Enrichment
select 'table: experiment, field: library_construction_protocol [ligation + enrichment]';
select '(study-exp join)experiment:library_construction_protocol', 'ligation+enrichment', count(*)
from
(
select
stu.study_accession id, count(library_construction_protocol) from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
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%"
or library_construction_protocol like "% a-tail%"
)
AND
(
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%"
)
group by id
);