- R package
optparse - Bioconductor packages
SRAdbGEOmetadb - (Optional--can be downloaded during first execution of
sraInfo.R) Pre-downloaded and uncompressedSRAmetadb.sqlite(seeSRAdbmanual) andGEOmetdb.sqlite(seeGEOmetadbmanual)
Get usage information
Rscript sraInfo.R -hExample usage
PREFIX=/home/cmb-01/as/jqu/sra_download
Rscript sraInfo.R -d ${PREFIX}/SRAmetadb.sqlite -m ${PREFIX}/GEOmetadb.sqlite -o ${PWD}/new_study -l ChIP-Seq SRP057141
An <Accession>.csv file containing the following columns:
| Column name | Example values |
|---|---|
| study | SRP057141 |
| submission | SRA258544 |
| sample | SRS908811 |
| experiment | SRX994293 |
| run | SRR1977542 |
| ftp | ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX994/SRX994293/SRR1977542/SRR1977542.sra |
| experiment_alias | human1_pachytene_H3K4me3 |
| sample_alias | human1_pachytene |
| scientific_name | Homo sapiens |
| library_name | human1_PS_K4 |
| library_strategy | ChIP-Seq |
| library_layout | SINGLE - |
| sample_attribute | isolate: BL2 || age: missing || biomaterial_provider: Dr. Sherman Silber, Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, MO, USA || sex: male || tissue: testis || cell_type: pachytene spermatocyte || phenotype: fertile || BioSampleModel: Human |
| title | NA |
The last column is the GEO GSM sample title, when sample_alias is a GSM accession.