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3 votes

What happened to sra ftp server?

SRA moved all of the data to the cloud per https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/24/sra-cloud/ You can still download data for free using sratoolkit as ...
vkkodali's user avatar
  • 1,266
3 votes
Accepted

Programmatically retrieve Metadata from SRA Run Selector

Depending on exactly which information you seek, you can try: esearch -db sra -query 'PRJNA491191[bioproject]' | efetch -format native -mode xml This will return ...
vkkodali's user avatar
  • 1,266
2 votes

Fixing FASTA file for Local BLAST Database

Briefly the best strategy I think is to download fastQ files and process this via an assembler. I wouldn't enter raw short read Illumina data into a local Blast database. What I'm pretty certain of is ...
M__'s user avatar
  • 12.6k
2 votes

What happened to sra ftp server?

NCBI appeared at least in part to shift onto Google Cloud buckets, one previous OP raised a question about access via GCP (I think the question was closed). Fundamentally, traditional FTP is not ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

Downloading multiple SRA files as FASTQ files using SRA Toolkit

That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-...
ATpoint's user avatar
  • 1,430
1 vote
Accepted

How to download Sequencing data on Windows using SRA toolkit?

I found a solution to this problem. After having installed SRA toolkit: prefetch -v SRR9....1 this helps download the SRA file. Then to extract it as FASTAQ ...
Sanjukta Ghosh's user avatar
1 vote

ZIP the fasterq-dump files in loop

I tried this and it worked ...
Shradha Sharma's user avatar
1 vote

ZIP the fasterq-dump files in loop

Haven't tried, but I believe you may add -Z to fasterq-dump and remove -k ${i} from gzip. In addition, I would recommend the ...
user172818's user avatar
  • 6,535

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