SRAdb vs SRAtools
How is SRAdb (an R package) different from SRA-toolkit (a command line interface) in terms of functionality?
For example, if I want to download all samples under some experiment, (say, all 404 samples for this experiment), can I use either tool?
1 answer
AFAIK due to enormous increase in size, SRAdb no longer provides access to current SRA data.
Your best bet is to use SRA-explorer to obtain fastq download URL's for the dataset you are looking for. Process of using the tool is described here: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Log in to answer this question.
More posts like this
-
Using GEOquery
written by Aryan •
-
SRA file identifiers for use with sra-toolkit
written by ScubaChris •
-
Error when reading microarray idat files from illumina
written by salamandra
-
NCBI GEO/GSM/SRA conventions: Is raw data a part of the SRA or a supplementary file?
written by abe •
-
Merge microarray datasetes with same platform
written by h72ghorashi •
-
Looking for DNase-seq of MCF10A cell line
written by bhchiang •
-
GEO (NCBI) confusing data
written by silas008
-
Peak Calling with MACS (treat and control samples)
written by ukpersia1 •
-
Tutorial: How to download raw sequence data from GEO/SRA
written by Obi Griffith
-
Normal Size Raw Data To Research, Cant Download Petabyte Of Zillion Reads
written by smagikern •
