Entering edit mode
8.1 years ago
me
▴
10
Once the SRA file from NCBI using prefetch -c <SRA number> has been downloaded...how do I see it's contents. Specifically, I want to see what columns/tables it has. No, I don't want the fasta/fastq files using fastq-dump, I want to actually get the movie metadata and .bax/.bas files from the PacBio sequencing run.
- How do I get these pieces of information?
- How do I see the columns/tables of the .sra file?
I know, but it just seems that this whole thing is fragmented. NCBI provides the SRA toolkit, but then it's different than the download file they provide in their link...and imo, there isn't enough documentation on this and the toolkit.
I think I must be missing something as I don't see how/why the SRA file would not contain the data which is clearly already on the record (in the "Download" tab). I assume this is in the SRA file under a table where we can retrieve it.
I had contacted SRA tech support about year back and this was their (paraphrased) response.
I am aware that PacBio hdf5 format is "not proprietary". But the above was what I had got from SRA support. You can ask them again, if anything has changed since.
Yet if we do
fastq-dump ---fastaof the SRA file, this fasta file would basically have all the sequenced reads from that run correct?That file should have all the reads that were generated from the raw data (*.h5) after processing with PacBio software (e.g. SMRTportal, "reads_of_insert" or "subreads", would depend on the analysis protocol used).
The data under the download tab is simply a link to the original compressed *.h5 files as provided by the submitters.
Given a list of SRR's and a little bit scripting one can build an automatic downloader based on this sort of command: