|Run||Spots||Bases||Size||GC content||Published||Access Type|
This run has 2 reads per spot:
|̅L=242, σ=62.8, 100%||̅L=232, σ=60.3, 100%|
Technical read Application Read L=4, 100% Length is 4, 100% spots contain this read ̅L=165, σ=92.8, 66% Average length is 165, standard deviation is 92.8, 66% spots contain this read
|PRJDB4543||DRP002875||Caridina multidentata genome and transcriptome sequencing|
Classical cadherins, a metazoan-specific subfamily of the cadherin superfamily, are homophilic cell-cell adhesion molecules that regulate tissue homeostasis and morphogenesis. Although the ectodomains of classical cadherins play conserved roles for homophilic binding interactions, their domain organizations show significant variations among metazoans. To exhaustively search the genome and transcripts of the decapod crustacean Caridina multidentata for genes encoding classical cadherins, we obtained sequence data from this species using an Illumina Miseq sequencer. The obtained sequences were analyzed by BLAST to find sequences related to classical cadherin cytoplasmic domains. The sequence data were also used for determining the structures of identified classical cadherin genes, including the exon-intron organizations.
You need SRA Toolkit to operate on SRA runs.
Default toolkit configuration enables it to find and retrieve SRA runs by accession. It also downloads (and cache) only the part of data you really need. For example quality scores represent a majority of data volume and you may not need them if you dump fasta only (versus fastq). Or if you are looking at particular gene you may not need reads aligned to other regions or not aligned at all. Same way if you use GATK with enabled SRA support you need only SRA run accessions to fire your process.
fastq-dump will dump reads in a number of "standard" fastq and fasta formats.
vdb-dump is also capable of producing fasta and fastq (beside other formats). It dumps data much faster then fastq-dump but ordering of reads may be different and it does not produce split-read multi-file output.
Prefetch tool will help you cache all data in advance if you plan to run data analysis in environment where getting data from NCBI at run time is unfeasible.
Read more at SRA Knowledge Base on how to download SRA data using command line utilities.