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Download files from Experiment Acession

Dear community,

I trying to dowload data from https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=769413 , here is the process I am doing:

  1. click on "send to" and choose file
  2. From this csv file a have a list with Experiment Acession which is a column with ids such as "SRX14461187"

Is there any programatic way that, given the ids download the file to machine?

Thank you and best regards

bioproject ncbi sra
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written by Manuel Sokolov Ravasqueira • Manuel Sokolov Ravasqueira

2 answers

Using Entrezdirect (only a couple example samples shown to save space there are 50+).

$ esearch -db bioproject -query PRJNA769413 | elink -target sra | efetch -format runinfo
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
SRR18323608,2022-03-30 16:13:57,2022-03-17 16:43:36,133934962,40180488600,133934962,300,14763,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR018/18323/SRR18323608/SRR18323608.lite.1,SRX14461185,Glutamate_neurons,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 4000,SRP340395,PRJNA769413,,769413,SRS12264843,SAMN26655248,simple,9606,Homo sapiens,Glutamate_neurons,,,,,male,,no,,,,,NIH NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES,SRA1384557,,public,A84D9173C49A5BB214079B6420195BAD,18E3A8257B7AF780CD5F26EF8A8305B0
SRR16235452,2022-03-14 11:26:30,2021-10-07 14:20:44,21415184,3212277600,21415184,150,1292,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR016/16235/SRR16235452/SRR16235452.lite.1,SRX12515387,LiPSC GR1.1_ Astro1_D30_1,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,NextSeq 550,SRP340395,PRJNA769413,,769413,SRS10477093,SAMN22133067,simple,9606,Homo sapiens,LiPSC GR1.1_ Astro1_D30_1,,,,,male,,no,,,,,NATIONAL EYE INSTITUTE,SRA1307558,,public,FF351F5D4F3C53A3D1561C264D980BC1,997A6E7D6753E8DB49EEA6E46AFC0F8B
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written by GenoMax GenoMax

Thank you so much, I was able to download the files saving the output of the line you gave me into a .csv

esearch -db bioproject -query PRJNA769413 | elink -target sra | efetch -format runinfo > results.csv

Then keep only the samples where LibraryStrategy == "RNA-seq" and finally using download_path to wget each link. However... this provides a ".lite.1" file.

The article https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(23)00236-9?uuid=uuid%3Ab6783c00-45f8-4af6-b583-09a27dc123e1#secsectitle0020 mentions that "Bulk RNA-seq and scRNA-seq, ATAC-seq, and MeDIP-seq FASTQ files have been deposited into the Sequence Read Archive (SRA) under BioProject PRJNA769413."

I really just wanted to download the scRNA-seq data to have a 10x matrix in the same way they start the analysis in the available code https://github.com/jaro-slamecka/Jovanovic_astrocyte_scRNA-seq/blob/main/Seurat.R GenoMax

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written by Manuel Sokolov Ravasqueira • Manuel Sokolov Ravasqueira

I really just wanted to download the scRNA-seq data to have a 10x matrix in the same way they start the analysis

Unfortunately you are not going to be able to do this using command line EntrezDirect (or other packages AFAIK). Submitter's do not appear to have published the count files on SRA (unless the paper provides some other location). You are going to to dump the fastq data from the file you downloaded.

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written by GenoMax GenoMax

Thank you GenoMax I solved it by doing wget for each file and then running 'fastq-dump' converting each .lite.1 to fastq, next step is to run cellranger to convert to counts matrix each file.

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written by Manuel Sokolov Ravasqueira • Manuel Sokolov Ravasqueira

https://nf-co.re/fetchngs/1.12.0/

Pipeline to fetch metadata and raw FastQ files from public databases

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written by Pierre Lindenbaum Pierre Lindenbaum

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