|Run||Spots||Bases||Size||GC content||Published||Access Type|
This run has 2 reads per spot:
|L=50, 100%||L=50, 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
|SAMEA962340 (ERS025088)||1x75 single mRNA-Seq2x50 PE mRNA-seq READ12x50 PE mRNA-seq READ2 Protocols: 1ug of total RNA was subjected to two rounds of oligo-dT beads binding. Purified mRNA was fragmented and random primed for cDNA synthesis. cDNA fragements were end repared, added dATP, and liagted to illumina pair end sample prep adaptor. The ligated material was amplified by PCR for 15 cycles, and used for illumina sequencing.||Homo sapiens|
SRA Toolkit tools directly operate on SRA runs. Toolkit has capacity to find requested runs at NCBI and download (and cache) only the part 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 the reads aligned to other regions or not aligned at all.
If you plan to run data analysis in environment where getting data from NCBI at run time is unfeasible you can use SRA Toolkit prefetch utility to cache all data in advance. Read more at SRA Knowledge Base on how to download SRA data using command line utilities.
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Taxonomy Analysis (alpha)
- experimental and error prone
- still short on documentation
- reference genomes are derived from refseq_genome blast database (which we do no claim to be perfect)
- uses 32-mers as base of comparision