How to extract metadata from NCBI's short read archive (SRA) for a few runs?

Question

I wish to extract metadata from a list of runs on NCBI's short read archive. For instance, I'd like to extract the library name ("HS0798") from the following run info:

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&run=SRR390728

I have to extract metadata for a few hundred run numbers. Is there a existing command-line tool (sratoolkit, python, perl, bash, etc) that will extract the metadata about the run?

I could grep it out of a webpage dump, but I notice there are XML schemas provided on the site, which to me indicates that there's some sort of XML API available somewhere.

using xslt, see an old answer I wrote for biostar: biostars.org/p/69974/#69995 — Pierre, Commented Feb 15, 2019 at 11:17

vkkodali · Accepted Answer · 2021-10-05 10:23:58Z

10

Entrez Direct is perfect for this sort of thing. You can do something like this:

$ esearch -db sra -query 'SRR390728' \
  | efetch -format runinfo \
  | cut -f1,12 -d,
Run,LibraryName
SRR292241,HS0798
SRR390728,HS0798

The runinfo table format has 47 fields including experiment accession, project accessions, bioproject and biosample identifiers and such. You may want to explore that a little bit more if you are interested in downloading metadata in addition to the LibraryName.

Also, if you prefer to parse XML output, you can append -mode xml to the efetch command to retrieve the runinfo table in XML format. xtract tool that comes with the Entrez Direct package can then be used to convert that into a table.

edited Oct 5, 2021 at 10:23

answered Feb 15, 2019 at 1:27

vkkodali

1,2866 silver badges9 bronze badges

$\begingroup$ Definitely better than my screen grab. I installed the conda package for sratools, which doesn't have that esearch binary with it. I'll have to look what package comes with that. $\endgroup$
– init_js
Commented Feb 15, 2019 at 2:27
2

$\begingroup$ Follow the installation instructions here: Entrez Direct. There is a package in Ubuntu repositories but it is quite behind from the latest version. $\endgroup$
– vkkodali
Commented Feb 15, 2019 at 11:52
$\begingroup$ But it seems that the runinfo is not the same as the RunTable found at this page: ncbi.nlm.nih.gov/Traces/study?. For example, go to the link and search for PRJNA301892. Under the "select" section (blue flag), there is a Metadata button. Is there a way to get that done? $\endgroup$
– M. Beausoleil
Commented Feb 18, 2020 at 21:15
$\begingroup$ The -q option is not valid with the version I just installed. -query should be used instead. $\endgroup$
– bli
Commented Oct 5, 2021 at 9:07
$\begingroup$ Thanks, I updated the answer to use -query now. $\endgroup$
– vkkodali
Commented Oct 5, 2021 at 10:24

Add a comment |

init_js · Accepted Answer · 2019-03-02 04:08:23Z

Here's a very crude script version, which should work without downloading fancy software tools. It will only work as long as the website stays in its current layout.

It extracts the particular <td> from the webpage, based on a nearby table link ID. and prints it out.

Note: This is brittle. It will only work for library names that fit in a single-line of the HTML, and will ignore some webserver errors. The content is also not html-decoded (so its output might show things like & if the field contained html-special characters).

#!/bin/bash

set -e -o pipefail

# pass the run as a single argument to the script
run="$1"

# extract library name field. second cell in visual order.
curl -o - "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&run=$run" 2>/dev/null | \
   grep 'a id="exp-accession"' -A 7 | \
   tail -n +3 | head -n 1 | \
   sed -e 's@^<td>@@' -e 's@</td>$@@'

M__ · Accepted Answer · 2019-02-14 19:39:45Z

1

Its got to be the SRA Toolkit The way I would do it (a traditional Perl digger) doesn't work on the Tracer NCBI site, at least not readily and dumping the XML is likewise unlikely to succeed.

answered Feb 14, 2019 at 19:39

M__♦

12.8k5 gold badges28 silver badges47 bronze badges

Add a comment |

init_js · Accepted Answer · 2019-05-31 20:54:27Z

I've been told by the support team that there's a way to pull it out in csv form by GETting the following URL, replacing <SRRNUMBER>, with, e.g. SRR000001:

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=<SRRNUMBER>

So this would be:

# download the file attachment
wget -nv -O foo.csv  "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRR000001"

# or just get the output on stdout
curl -v "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRR000001"

As an example, the output looks like this for SRR000001. It namely contains additional info on other runs from the same SRX:

Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR000001,2008-04-04 14:36:13,2015-04-07 21:54:15,470985,129515135,236041,274,298,,https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/000000/SRR000001,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,25D46C95842BCD2F235DDD48070341C4,5FC1B56C9A5332BD21A6FCC6713C3159
SRR000013,2008-04-04 15:15:44,2012-01-19 15:14:06,478304,131410350,316908,274,307,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000013,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,A576F73351E329617F91C92845ADE3BE,0EFE27254FB8790C80E4A8A3A3CCBF1D
SRR000019,2008-04-04 15:20:15,2012-01-19 15:14:06,537808,147928455,358612,275,347,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000019,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,5E42E66B2972A28C3C1B714499B3CE1E,A44F729DF562E11BDA4F950F171085B3
SRR000033,2008-04-04 15:26:19,2012-01-19 15:14:16,476737,131230950,316780,275,307,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000033,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,8D775F0FB1E78F2818166B4E6C7BC320,6C794108B0172AE98323C9A809BE892E
SRR000047,2008-04-04 15:34:57,2012-01-19 15:14:25,322279,88301883,214744,273,208,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000047,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,B4D7BC3DAD22AE58EADC18B2F05B2732,154C9532706F955A63CF685C4D71D9E6
SRR000049,2008-04-04 15:35:58,2012-01-19 15:14:34,506408,139029601,328595,274,336,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000049,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,60D02918CD7686DA084607BFD9D8E6A5,E9A732F2A8F36B8EB1CD38CA41BA8FB5
SRR000061,2008-04-04 15:41:48,2012-01-19 15:14:37,532884,146330433,351541,274,348,,https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/000000/SRR000061,SRX000007,SID2748,WGS,RANDOM,GENOMIC,PAIRED,3000,0,LS454,454 GS FLX,SRP000001,PRJNA33627,1,33627,SRS000100,SAMN00001583,simple,9606,Homo sapiens,NA18505,,,,,female,,no,,,,,454MSC,SRA000197,,public,8F6E1CA597BCAA19A852036775FA1FAB,2C035CCBD62808A01CEF6EB13BAEB40F

Providing an invalid SRR number will generate an empty HTTP 200 response.

user2268user2268 · Accepted Answer · 2020-01-07 21:00:57Z

0

Not a command-line tool but also useful is redesigned SRA Run Selector. Insert comma separated accessions and you can filter/download based on metadata.

answered Jan 7, 2020 at 21:00

user2268

Add a comment |

Saket Choudhary · Accepted Answer · 2020-01-22 23:06:16Z

You can get metadata for an entire project using pysradb:

> pysradb metadata SRP063732 --detailed

study_accession experiment_accession experiment_title                                                       experiment_desc                                                        organism_taxid  organism_name   library_strategy library_source library_selection sample_accession sample_title instrument           total_spots total_size   run_accession run_total_spots run_total_bases run_alias             sra_url                                                                                 experiment_alias isolate                 dev_stage sex   tissue             treatment     BioSampleModel           
 SRP063732       SRX1249861           Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26168_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071080                    Illumina HiSeq 2000  89051187    11830170462  SRR2420581    89051187        17988339774     26168_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420581/SRR2420581.1                   26168_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249860           Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 26148_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071081                    Illumina HiSeq 2000  87335402    11763248173  SRR2420580    87335402        17641751204     26148_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420580/SRR2420580.1                   26148_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249859           Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25822_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071082                    Illumina HiSeq 2000  83544130    9481342835   SRR2420579    83544130        13784781450     25822_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420579/SRR2420579.1                   25822_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249858           Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 25154_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071083                    Illumina HiSeq 2000  115476876   13003165573  SRR2420578    115476876       19053684540     25154_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420578/SRR2420578.1                   25154_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249857           Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23784_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071084                    Illumina HiSeq 2000  101539017   13697691917  SRR2420577    101539017       20510881434     23784_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420577/SRR2420577.1                   23784_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249856           Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23779_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071085                    Illumina HiSeq 2000  98394582    13326784419  SRR2420576    98394582        19875705564     23779_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420576/SRR2420576.1                   23779_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249855           Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23773_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071086                    Illumina HiSeq 2000  84442355    11218164664  SRR2420575    84442355        17057355710     23773_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420575/SRR2420575.1                   23773_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249854           Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23764_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071087                    Illumina HiSeq 2000  87197006    11291883405  SRR2420574    87197006        17613795212     23764_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420574/SRR2420574.1                   23764_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249853           Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  Bisulfite-seq of rhesus macaque 23762_HeavyDrinker: Nucleus accumbens  9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071088                    Illumina HiSeq 2000  89455608    11917710767  SRR2420573    89455608        18070032816     23762_NaC_HD_files    https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420573/SRR2420573.1                   23762_NucleusAccumbens  Adult     male  Nucleus accumbens  HeavyEthanol  Model organism or animal
 SRP063732       SRX1249852           Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25811_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071089                    Illumina HiSeq 2000  88216999    10285962574  SRR2420572    88216999        14555804835     25811_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420572/SRR2420572.1                   25811_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249851           Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25790_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071090                    Illumina HiSeq 2000  94731241    10748979142  SRR2420571    94731241        15630654765     25790_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420571/SRR2420571.1                   25790_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249850           Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25742_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071091                    Illumina HiSeq 2000  113512952   17943763654  SRR2420570    113512952       22929616304     25742_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420570/SRR2420570.1                   25742_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249849           Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25240_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071092                    Illumina HiSeq 2000  81002663    9232986327   SRR2420569    81002663        13365439395     25240_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420569/SRR2420569.1                   25240_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249848           Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25184_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071093                    Illumina HiSeq 2000  110228135   12594727479  SRR2420568    110228135       18187642275     25184_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420568/SRR2420568.1                   25184_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249847           Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 25157_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071094                    Illumina HiSeq 2000  97249804    11026452312  SRR2420567    97249804        16046217660     25157_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420567/SRR2420567.1                   25157_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249846           Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    Bisulfite-seq of rhesus macaque 21119_LowDrinker: Nucleus accumbens    9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071095                    Illumina HiSeq 2000  68899204    9241244635   SRR2420566    68899204        13917639208     21119_NaC_LMD _files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420566/SRR2420566.1                   21119_NucleusAccumbens  Adult     male  Nucleus accumbens  LightEthanol  Model organism or animal
 SRP063732       SRX1249845           Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26104_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071096                    Illumina HiSeq 2000  84859783    9604170375   SRR2420565    84859783        14001864195     26104_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420565/SRR2420565.1                   26104_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249844           Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 26082_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071097                    Illumina HiSeq 2000  73346886    8248399265   SRR2420564    73346886        12102236190     26082_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420564/SRR2420564.1                   26082_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249843           Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25207_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071098                    Illumina HiSeq 2000  77306973    12235827725  SRR2420563    77306973        15616008546     25207_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420563/SRR2420563.1                   25207_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249842           Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 25407_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071099                    Illumina HiSeq 2000  83985968    13355795218  SRR2420562    83985968        16965165536     25407_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420562/SRR2420562.1                   25407_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249841           Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24818_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071100                    Illumina HiSeq 2000  72782928    8484613123   SRR2420561    72782928        12009183120     24818_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420561/SRR2420561.1                   24818_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249840           Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24698_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071101                    Illumina HiSeq 2000  79414016    12627204820  SRR2420560    79414016        16041631232     24698_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420560/SRR2420560.1                   24698_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249839           Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 24340_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071102                    Illumina HiSeq 2000  84772576    13436053136  SRR2420559    84772576        17124060352     24340_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420559/SRR2420559.1                   24340_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal
 SRP063732       SRX1249838           Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       Bisulfite-seq of rhesus macaque 22770_Control: Nucleus accumbens       9544            Macaca mulatta  Bisulfite-Seq    GENOMIC        other             SRS1071103                    Illumina HiSeq 2000  83310630    13224887149  SRR2420558    83310630        16828747260     22770_NaC_Ctrl_files  https://sra-download.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2420558/SRR2420558.1                   22770_NucleusAccumbens  Adult     male  Nucleus accumbens  Control       Model organism or animal

Stack Exchange Network

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

6 Answers 6

Your Answer

Not the answer you're looking for? Browse other questions tagged
phylogenetics
sratoolkit
or ask your own question.

Hot Network Questions

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

6 Answers 6

Your Answer

Sign up or log in

Post as a guest

Not the answer you're looking for? Browse other questions tagged phylogeneticssratoolkit or ask your own question.

Related

Hot Network Questions

Not the answer you're looking for? Browse other questions tagged
phylogenetics
sratoolkit
or ask your own question.