Is there a tool like "pacbio-dump" for SRAToPacbio?

pb-jlandolin / PacbioToSRA

Take a list of Pacbio files (.fofn) and creates a spreadsheet for data submission to the sequuence read archive (SRA)

Other

13 stars 4 forks source link

Is there a tool like "pacbio-dump" for SRAToPacbio? #2

Open RyanBio opened 7 years ago

RyanBio commented 7 years ago

Hi, @pb-jlandolin I download some test data from the ncbi, as the sra-tools do not provide a "pacbio-dump" like fastq-dump or illumina-dump, I used the commod "fastq-dump --table SEQUENCE *.sra" . But the sequence are all raw ZMW reads before filtering low quality and cutting adapters. My questions:

Is there a tool like "pacbio-dump" to extract the raw data (bax.h5) from sra data?
Or is there a tool to distinguish the pacbio adapters in raw ZMW reads ?

Best Ryan

pb-jlandolin commented 7 years ago

There is no pacbio-dump script. What you need to do is click on the SRR id, then click on the "Download" tab, and download the original bax.h5 files instead of the .sra files: