Last updated: 2024-07-25
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a0610af | Dave Tang | 2024-07-25 | Add intro and example query |
| html | 1dbd4f3 | Dave Tang | 2024-07-25 | Build site. |
| Rmd | 39a6fe8 | Dave Tang | 2024-07-25 | Querying the SRA |
The SRAdb package is a compilation of metadata from NCBI SRA and tools. Specifically:
The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools.
SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful.
fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
First download SRAmetadb.sqlite.gz and gunzip it; the
function getSRAdbFile() can do this but I recommend
downloading this file externally. The gzipped file is around 6.8G in
size (2024-07-26) and when uncompressed is 138G in size.
sqlfile <- getSRAdbFile(method = "wget")Download database file externally using wget.
wget -c https://gbnci.cancer.gov/backup/SRAmetadb.sqlite.gzPoint to the location of downloaded and gunzipped file.
sqlfile <- '/data2/sradb/SRAmetadb.sqlite'Create a connection for queries. The standard DBI functionality as implemented in RSQLite function dbConnect makes the connection to the database. The dbDisconnect function disconnects the connection.
sra_con <- dbConnect(SQLite(), sqlfile)Database tables.
sra_tables <- dbListTables(sra_con)
sra_tables [1] "col_desc" "experiment" "metaInfo" "run"
[5] "sample" "sra" "sra_ft" "sra_ft_content"
[9] "sra_ft_segdir" "sra_ft_segments" "study" "submission" Study fields.
dbListFields(sra_con, "study") [1] "study_ID" "study_alias" "study_accession"
[4] "study_title" "study_type" "study_abstract"
[7] "broker_name" "center_name" "center_project_name"
[10] "study_description" "related_studies" "primary_study"
[13] "sra_link" "study_url_link" "xref_link"
[16] "study_entrez_link" "ddbj_link" "ena_link"
[19] "study_attribute" "submission_accession" "sradb_updated" Query.
rs <- dbGetQuery(sra_con, "select * from study limit 3")
rs[, 1:3] study_ID study_alias study_accession
1 1 DRP000001 DRP000001
2 2 DRP000002 DRP000002
3 3 DRP000003 DRP000003How do we get the SRR accession for SRX510365? (Should be SRR1216135)
my_id <- 'SRX510365'
conversion <- sraConvert(my_id, sra_con = sra_con)
conversion experiment submission study sample run
1 SRX510365 SRA090948 SRP025982 SRS588883 SRR1216135Disconnect.
dbDisconnect(conn = sra_con)
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SRAdb_1.66.0 RCurl_1.98-1.14 graph_1.82.0
[4] BiocGenerics_0.50.0 RSQLite_2.3.7 lubridate_1.9.3
[7] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[10] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[16] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.5 xfun_0.44 bslib_0.7.0 processx_3.8.4
[5] Biobase_2.64.0 callr_3.7.6 tzdb_0.4.0 bitops_1.0-7
[9] vctrs_0.6.5 tools_4.4.0 ps_1.7.6 generics_0.1.3
[13] stats4_4.4.0 fansi_1.0.6 blob_1.2.4 pkgconfig_2.0.3
[17] data.table_1.15.4 lifecycle_1.0.4 compiler_4.4.0 git2r_0.33.0
[21] statmod_1.5.0 munsell_0.5.1 getPass_0.2-4 httpuv_1.6.15
[25] htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.8 later_1.3.2
[29] pillar_1.9.0 jquerylib_0.1.4 whisker_0.4.1 limma_3.60.4
[33] cachem_1.1.0 tidyselect_1.2.1 digest_0.6.35 stringi_1.8.4
[37] rprojroot_2.0.4 fastmap_1.2.0 grid_4.4.0 GEOquery_2.72.0
[41] colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3 utf8_1.2.4
[45] withr_3.0.0 scales_1.3.0 promises_1.3.0 bit64_4.0.5
[49] timechange_0.3.0 rmarkdown_2.27 httr_1.4.7 bit_4.0.5
[53] hms_1.1.3 memoise_2.0.1 evaluate_0.24.0 knitr_1.47
[57] rlang_1.1.4 Rcpp_1.0.12 glue_1.7.0 DBI_1.2.3
[61] xml2_1.3.6 rstudioapi_0.16.0 jsonlite_1.8.8 R6_2.5.1
[65] fs_1.6.4