Case Studies#
Case Study 1#
Consider a scenario where somone is interested in searching for single-cell RNA-seq datasets. In particular, the interest is in studying retina:
$ pysradb search --query "single-cell rna-seq retina"
study_accession experiment_accession experiment_title sample_taxon_id sample_scientific_name experiment_library_strategy experiment_library_source experiment_library_selection sample_accession sample_alias experiment_instrument_model pool_member_spots run_1_size run_1_accession run_1_total_spots run_1_total_bases
SRP299803 SRX9756769 GSM4995565: scATAC_Retina_WT; Mus musculus; ATAC-seq 10090 Mus musculus ATAC-seq GENOMIC other SRS7946094 GSM4995565 Illumina NovaSeq 6000 55435867 2637580797 SRR13329759 55435867 6874047508
SRP299803 SRX9756768 GSM4995564: scRNA_Retina_VSX2SEKO_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7946093 GSM4995564 Illumina NovaSeq 6000 96123725 4107807391 SRR13329758 96123725 12688331700
SRP299803 SRX9756767 GSM4995563: scRNA_Retina_VSX2SEKO_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7946092 GSM4995563 Illumina NovaSeq 6000 94345783 4056010488 SRR13329757 94345783 12453643356
SRP299803 SRX9756766 GSM4995562: scRNA_Retina_WT_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7946091 GSM4995562 Illumina NovaSeq 6000 99487074 4240172698 SRR13329756 99487074 13132293768
SRP299803 SRX9756765 GSM4995561: scRNA_Retina_WT_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7946090 GSM4995561 Illumina NovaSeq 6000 88048461 3817540828 SRR13329755 88048461 11622396852
SRP257758 SRX9537754 GSM4916438: Pou4f2-tdTomato/+ E17.5 scRNA-seq; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7743995 GSM4916438 Illumina HiSeq 2500 364683840 8246658699 SRR13091939 364683840 32456861760
SRP257758 SRX9537753 GSM4916437: Atoh7-zsGreen/lacZ E17.5 scRNA-seq; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7743994 GSM4916437 Illumina HiSeq 2500 530456067 11895864680 SRR13091938 530456067 47210589963
SRP257758 SRX9537752 GSM4916436: Atoh7-zsGreen/+ E17.5 scRNA-seq; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7743993 GSM4916436 Illumina HiSeq 2500 389849416 8671923722 SRR13091937 389849416 34696598024
SRP257758 SRX9537751 GSM4916435: Atoh7-zsGreen/lacZ E14.5 scRNA-seq; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7743992 GSM4916435 Illumina HiSeq 2500 328878355 7875737709 SRR13091936 328878355 29270173595
SRP257758 SRX9537750 GSM4916434: Atoh7-zsGreen/+ E14.5 scRNA-seq; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS7743991 GSM4916434 Illumina HiSeq 2500 522040155 12760941656 SRR13091935 522040155 46461573795
ERP118072 ERX3614517 NextSeq 500 sequencing; 3' mRNA-seq of protrusions and cell bodies of BJ, PC-3M, RPE-1, U-87 and WM-266.4 cells 9606 Homo sapiens OTHER TRANSCRIPTOMIC Oligo-dT ERS3920269 SAMEA6120013 NextSeq 500 5818488 43355751 ERR3619129 1457318 109897743
ERP118072 ERX3614516 NextSeq 500 sequencing; 3' mRNA-seq of protrusions and cell bodies of BJ, PC-3M, RPE-1, U-87 and WM-266.4 cells 9606 Homo sapiens OTHER TRANSCRIPTOMIC Oligo-dT ERS3920268 SAMEA6120012 NextSeq 500 5422441 40645479 ERR3619125 1359663 102468758
SRP288715 SRX9369597 RPE1_SS119_p10 9606 Homo sapiens OTHER GENOMIC other SRS7591452 RPE1_SS119_p10.bam Illumina HiSeq 2000 5062938 88426773 SRR12904705 5062938 202517520
SRP288715 SRX9369596 RPE1_SS119_p0 9606 Homo sapiens OTHER GENOMIC other SRS7591451 RPE1_SS119_p0.bam Illumina HiSeq 2000 978835 19219630 SRR12904706 978835 39153400
SRP288715 SRX9369595 RPE1_SS111_p10 9606 Homo sapiens OTHER GENOMIC other SRS7591450 RPE1_SS111_p10.bam Illumina HiSeq 2000 6205827 108129733 SRR12904707 6205827 248233080
SRP288715 SRX9369594 RPE1_SS111_p0 9606 Homo sapiens OTHER GENOMIC other SRS7591449 RPE1_SS111_p0.bam Illumina HiSeq 2000 928703 18488436 SRR12904708 928703 37148120
SRP288715 SRX9369593 RPE1_SS51_p10 9606 Homo sapiens OTHER GENOMIC other SRS7591448 RPE1_SS51_p10.bam Illumina HiSeq 2000 6088168 106065537 SRR12904709 6088168 243526720
SRP288715 SRX9369592 RPE1_SS51_p0 9606 Homo sapiens OTHER GENOMIC other SRS7591447 RPE1_SS51_p0.bam Illumina HiSeq 2000 1624227 30610200 SRR12904710 1624227 64969080
SRP288715 SRX9369591 RPE1_SS48_p10 9606 Homo sapiens OTHER GENOMIC other SRS7591446 RPE1_SS48_p10.bam Illumina HiSeq 2000 8117881 139408135 SRR12904711 8117881 324715240
SRP288715 SRX9369590 RPE1_SS48_p0 9606 Homo sapiens OTHER GENOMIC other SRS7591445 RPE1_SS48_p0.bam Illumina HiSeq 2000 776140 15821200 SRR12904712 776140 31045600
By default search returns first 20 hits. SRP299803 seems like a
project of interest. However the information outputted by the search
command is pretty limited. We want to look up more detailed information
about this project:
$ pysradb metadata SRP299803 | head
study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title instrument instrument_model instrument_model_desc total_spots total_size run_accession run_total_spots run_total_bases
SRP299803 SRX9756769 GSM4995565: scATAC_Retina_WT; Mus musculus; ATAC-seq GSM4995565: scATAC_Retina_WT; Mus musculus; ATAC-seq 10090 Mus musculus ATAC-seq GENOMIC other PAIRED SRS7946094 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 55435867 2637580797 SRR13329759 55435867 6874047508
SRP299803 SRX9756768 GSM4995564: scRNA_Retina_VSX2SEKO_Rep2; Mus musculus; RNA-Seq GSM4995564: scRNA_Retina_VSX2SEKO_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946093 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 96123725 4107807391 SRR13329758 96123725 12688331700
SRP299803 SRX9756767 GSM4995563: scRNA_Retina_VSX2SEKO_Rep1; Mus musculus; RNA-Seq GSM4995563: scRNA_Retina_VSX2SEKO_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946092 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 94345783 4056010488 SRR13329757 94345783 12453643356
SRP299803 SRX9756766 GSM4995562: scRNA_Retina_WT_Rep2; Mus musculus; RNA-Seq GSM4995562: scRNA_Retina_WT_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946091 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 99487074 4240172698 SRR13329756 99487074 13132293768
SRP299803 SRX9756765 GSM4995561: scRNA_Retina_WT_Rep1; Mus musculus; RNA-Seq GSM4995561: scRNA_Retina_WT_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946090 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 88048461 3817540828 SRR13329755 88048461 11622396852
It is also possible to get more detailed information using the
--detailed flag:
$ pysradb metadata SRP075720 --detailed
run_accession study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title instrument instrument_model instrument_model_desc total_spots total_size run_total_spots run_total_bases run_alias sra_url experiment_alias source_name strain background genotype tissue/cell type molecule subtype ena_fastq_http ena_fastq_http_1 ena_fastq_http_2 ena_fastq_ftp ena_fastq_ftp_1 ena_fastq_ftp_2
SRR13329759 SRP299803 SRX9756769 GSM4995565: scATAC_Retina_WT; Mus musculus; ATAC-seq GSM4995565: scATAC_Retina_WT; Mus musculus; ATAC-seq 10090 Mus musculus ATAC-seq GENOMIC other PAIRED SRS7946094 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 55435867 2637580797 55435867 6874047508 GSM4995565_r1 https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/013017/SRR13329759 GSM4995565 wild type_retina C57BL/6 wild type retina http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/059/SRR13329759/SRR13329759_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/059/SRR13329759/SRR13329759_2.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/059/SRR13329759/SRR13329759_1.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/059/SRR13329759/SRR13329759_2.fastq.gz
SRR13329758 SRP299803 SRX9756768 GSM4995564: scRNA_Retina_VSX2SEKO_Rep2; Mus musculus; RNA-Seq GSM4995564: scRNA_Retina_VSX2SEKO_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946093 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 96123725 4107807391 96123725 12688331700 GSM4995564_r1 https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/013017/SRR13329758 GSM4995564 Vsx2SE Δ/Δ_retina C57BL/6 Vsx2SE {delta}/{delta} retina 3' RNA http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/058/SRR13329758/SRR13329758_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/058/SRR13329758/SRR13329758_2.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/058/SRR13329758/SRR13329758_1.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/058/SRR13329758/SRR13329758_2.fastq.gz
SRR13329757 SRP299803 SRX9756767 GSM4995563: scRNA_Retina_VSX2SEKO_Rep1; Mus musculus; RNA-Seq GSM4995563: scRNA_Retina_VSX2SEKO_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946092 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 94345783 4056010488 94345783 12453643356 GSM4995563_r1 https://sra-download.ncbi.nlm.nih.gov/traces/sra79/SRR/013017/SRR13329757 GSM4995563 Vsx2SE Δ/Δ_retina C57BL/6 Vsx2SE {delta}/{delta} retina 3' RNA http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/057/SRR13329757/SRR13329757_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/057/SRR13329757/SRR13329757_2.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/057/SRR13329757/SRR13329757_1.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/057/SRR13329757/SRR13329757_2.fastq.gz
SRR13329756 SRP299803 SRX9756766 GSM4995562: scRNA_Retina_WT_Rep2; Mus musculus; RNA-Seq GSM4995562: scRNA_Retina_WT_Rep2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946091 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 99487074 4240172698 99487074 13132293768 GSM4995562_r1 https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/013017/SRR13329756 GSM4995562 wild type_retina C57BL/6 wild type retina 3' RNA http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/056/SRR13329756/SRR13329756_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/056/SRR13329756/SRR13329756_2.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/056/SRR13329756/SRR13329756_1.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/056/SRR13329756/SRR13329756_2.fastq.gz
SRR13329755 SRP299803 SRX9756765 GSM4995561: scRNA_Retina_WT_Rep1; Mus musculus; RNA-Seq GSM4995561: scRNA_Retina_WT_Rep1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA PAIRED SRS7946090 Illumina NovaSeq 6000 Illumina NovaSeq 6000 ILLUMINA 88048461 3817540828 88048461 11622396852 GSM4995561_r1 https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/013017/SRR13329755 GSM4995561 wild type_retina C57BL/6 wild type retina 3' RNA http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/055/SRR13329755/SRR13329755_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/055/SRR13329755/SRR13329755_2.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/055/SRR13329755/SRR13329755_1.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR133/055/SRR13329755/SRR13329755_2.fastq.gz
Having made sure this dataset is indeed of interest, we want to save some work and see if the processed dataset has been made available on GEO by the authors:
$ pysradb srp-to-gse SRP299803
study_accession study_alias
SRP299803 GSE164044
So indeed a GEO project exists for this SRA dataset.
Notice, that the GEO information was also visible in the
metadata --detailed operation. Assume we were in posession of the GSM
id of one of the experiments to start off with, say GSE4995565.
Starting from this GSM id, we want to get the following information:
SRP id of the project
GSE id of the project
SRX id of the experiment
SRR id(s) corresponding to the experiment
Get SRP id:
$ pysradb gsm-to-srp GSM4995565
experiment_alias study_accession
GSM4995565 SRP299803
Get GSE id:
$ pysradb gsm-to-gse GSM4995565
experiment_alias study_alias
GSM4995565 GSE164044
Get SRX id:
$ pysradb gsm-to-srx GSM4995565
experiment_alias experiment_accession
GSM4995565 SRX9756769
Getting SRR id(s):
$ pysradb gsm-to-srr GSM4995565
experiment_alias run_accession
GSM4995565 SRR13329759
Case Study 2#
Our first case study included metadata search. Next, we explore downloading datasets.
We have a SRP id to start off with: SRP000941. We want to quickly
checkout its contents:
$ pysradb metadata SRP000941 --detailed| head
study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy library_source library_selection library_layout sample_accession sample_title instrument instrument_model instrument_model_desc total_spots total_size run_accession run_total_spots run_total_bases
SRP000941 SRX056722 Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells 9606 Homo sapiens SAK270 ChIP-Seq GENOMIC ChIP SINGLE SRS184466 Illumina HiSeq 2000 Illumina HiSeq 2000 ILLUMINA 26900401 531654480 SRR179707 26900401 807012030
SRP000941 SRX027889 Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells 9606 Homo sapiens SAK201 ChIP-Seq GENOMIC ChIP SINGLE SRS116481 Illumina Genome Analyzer II Illumina Genome Analyzer II ILLUMINA 37528590 779578968 SRR067978 37528590 1351029240
SRP000941 SRX027888 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens LLH1U ChIP-Seq GENOMIC RANDOM SINGLE SRS116483 Illumina Genome Analyzer II Illumina Genome Analyzer II ILLUMINA 13603127 3232309537 SRR067977 13603127 489712572
SRP000941 SRX027887 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens DM219 ChIP-Seq GENOMIC RANDOM SINGLE SRS116562 Illumina Genome Analyzer II Illumina Genome Analyzer II ILLUMINA 22430523 506327844 SRR067976 22430523 807498828
This project is a collection of multiple assays.
$ pysradb metadata SRP000941 --detailed | tr -s ' ' | cut -f5 -d ' ' | sort | uniq -c
999 Bisulfite-Seq
768 ChIP-Seq
1 library_strategy
121 OTHER
353 RNA-Seq
28 WGS
We want to however only download RNA-seq samples:
$ pysradb metadata SRP000941 --detailed | grep 'study\|RNA-Seq' | pysradb download
This will download all RNA-seq samples coming from this project using
aspera-client, if available. Alternatively, it can also use wget.
Downloading an entire project is easy:
$ pysradb download -p SRP000941
Downloads are organized by SRP/SRX/SRR mimicking the hiererachy of SRA
projects.