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Rmd 39a6fe8 Dave Tang 2024-07-25 Querying the SRA

SRAdb

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.

SQLite database

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.gz

Point 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)

SRA tables

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"       

Sample fields.

dbListFields(sra_con, "sample")
 [1] "sample_ID"            "sample_alias"         "sample_accession"    
 [4] "broker_name"          "center_name"          "taxon_id"            
 [7] "scientific_name"      "common_name"          "anonymized_name"     
[10] "individual_name"      "description"          "sra_link"            
[13] "sample_url_link"      "xref_link"            "sample_entrez_link"  
[16] "ddbj_link"            "ena_link"             "sample_attribute"    
[19] "submission_accession" "sradb_updated"       

Query.

rs <- dbGetQuery(sra_con, "select * from study limit 3")
rs[, 1:5]
  study_ID study_alias study_accession
1        1   DRP000001       DRP000001
2        2   DRP000002       DRP000002
3        3   DRP000003       DRP000003
                                                                                study_title
1                          Bacillus subtilis subsp. natto BEST195 genome sequencing project
2                       Model organism for prokaryotic cell differentiation and development
3 Comprehensive identification and characterization of the nucleosome             structure
               study_type
1 Whole Genome Sequencing
2 Whole Genome Sequencing
3  Transcriptome Analysis

Query matching specific study accession.

dbGetQuery(sra_con, "select * from study where study_accession == 'DRP000001'")
  study_ID study_alias study_accession
1        1   DRP000001       DRP000001
                                                       study_title
1 Bacillus subtilis subsp. natto BEST195 genome sequencing project
               study_type
1 Whole Genome Sequencing
                                                                                                                                                                                           study_abstract
1 <b><i>Bacillus subtilis</i> subsp. <i>natto</i> BEST195</b>. i>Bacillus subtilis</i> subsp. <i>natto</i> BEST195 was isolated from fermented soybeans and will be used for comparative genome analysis.
  broker_name center_name                    center_project_name
1        <NA>        KEIO Bacillus subtilis subsp. natto BEST195
  study_description related_studies primary_study sra_link study_url_link
1              <NA>            <NA>          <NA>     <NA>           <NA>
                             xref_link study_entrez_link ddbj_link ena_link
1 pubmed: 20398357 || pubmed: 25329997              <NA>      <NA>     <NA>
  study_attribute submission_accession       sradb_updated
1            <NA>            DRA000001 2023-12-03 23:10:21

Match a list of study accessions.

rs <- dbGetQuery(sra_con, "select * from study where study_accession in ('DRP000001', 'DRP000003')")
rs[, 1:5]
  study_ID study_alias study_accession
1        1   DRP000001       DRP000001
2        3   DRP000003       DRP000003
                                                                                study_title
1                          Bacillus subtilis subsp. natto BEST195 genome sequencing project
2 Comprehensive identification and characterization of the nucleosome             structure
               study_type
1 Whole Genome Sequencing
2  Transcriptome Analysis

SRX to SRR

How do we get the SRR accession for SRX510365? (Should be SRR1216135)

exps <- c("SRX510281", "SRX510280", "SRX510279", "SRX510278", "SRX510277", "SRX510276")

lookup <- sraConvert(exps, sra_con = sra_con)
lookup
  experiment submission     study    sample        run
1  SRX510276  SRA090948 SRP025982 SRS588793 SRR1216046
2  SRX510277  SRA090948 SRP025982 SRS588794 SRR1216047
3  SRX510278  SRA090948 SRP025982 SRS588795 SRR1216048
4  SRX510279  SRA090948 SRP025982 SRS588796 SRR1216049
5  SRX510280  SRA090948 SRP025982 SRS588798 SRR1216050
6  SRX510281  SRA090948 SRP025982 SRS588797 SRR1216051

Get sample information.

purrr::map_df(lookup$sample, \(x){
  dbGetQuery(sra_con, paste0("select * from sample where sample_accession == '", x, "'"))
})$sample_attribute
[1] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L03 || barcode: TAGCTT || flowcell: AC132FACXX"
[2] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L04 || barcode: TAGCTT || flowcell: AC132FACXX"
[3] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L05 || barcode: TAGCTT || flowcell: AC132FACXX"
[4] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L06 || barcode: TAGCTT || flowcell: AC132FACXX"
[5] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L07 || barcode: TAGCTT || flowcell: AC132FACXX"
[6] "source_name: Human Brain Reference RNA (HBRR) from Ambion || seqc sample: B || platform: Illumina HiSeq 2000 || site: NYG || library id: 4 || lane: L08 || barcode: TAGCTT || flowcell: AC132FACXX"

End

Disconnect.

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