SRA queries

Serratus SRA Seach Queries

These are the SRA search queries used to generate the sraRunInfo.csv files which have been completed. This is a de-facto manifest of the search space.

s3://lovelywater/sra/
├ hu_SraRunInfo.csv.gz      # human (pulic)
├ hu_meta_SraRunInfo.csv.gz # human meta-genomic (public)
├ mu_SraRunInfo.csv.gz      # mouse
├ mamm_SraRunInfo.csv.gz    # mammalian
├ vert_SraRunInfo.csv.gz    # vertebrate
├ viro_SraRunInfo.csv.gz    # virome
└ sra.md5                   # md5sum for SraRunInfo.csv files 

Human (public)

• File: hu_SraRunInfo.csv

Search Term:

"txid9606"[Organism:exp] AND ("type_rnaseq"[Filter]) AND cluster_public[prop] AND "platform illumina"[Properties]

SRA Accessed: 2020/05/30

Results: 572215

AND

• File: hu_meta_SraRunInfo.csv

Search Term:

"txid9606"[Organism:exp] AND ("metagenomic"[Filter] OR "metatranscriptomic"[Filter]) AND cluster_public[prop] AND "platform illumina"[Properties]

SRA Accessed: 2020/05/30

Results: 36052

Mouse

• File: mu_SraRunInfo.csv

Search Term:

("Mus musculus"[orgn]) AND ("type_rnaseq"[Filter] OR "metagenomic"[Filter] OR "metatranscriptomic"[Filter]) AND "platform illumina"[Properties]

SRA Accessed: 2020/06/06

Results: 594949

Mammalian

• File: mamm_SraRunInfo.csv

Search Term:

("Mammalia"[Organism] NOT "Homo sapiens"[Organism] NOT "Mus musculus"[orgn]) AND ("type_rnaseq"[Filter] OR "metagenomic"[Filter] OR "metatranscriptomic"[Filter]) AND "platform illumina"[Properties]

SRA Accessed: 2020/06/06

Results: 82367

Vertebrate

• File: vert_SraRunInfo.csv

Search Term:

("Vertebrata"[Organism] NOT "Mammalia"[Organism] NOT "Homo sapiens"[Organism] NOT "Mus musculus"[orgn]) AND ("type_rnaseq"[Filter] OR "metagenomic"[Filter] OR "metatranscriptomic"[Filter]) AND cluster_public[prop] AND "platform illumina"[Properties]

SRA Accessed: 2020/05/25

Results: 86934

Virome

• File: viro_SraRunInfo.csv

Search Term:

(virome) AND cluster_public[prop] AND "platform illumina"[Properties]

SRA Accessed: 2020/05/28

Results: 8467

README Mirrors

• readme: https://github.com/ababaian/serratus/wiki/SRA-queries
• readme mirror: s3://lovelywater/sra/README.md