biostar-central VS sra-tools

Biostars is a great community, basically a bioinformatics-focused version of stackoverflow.

Go here: https://www.biostars.org/

Biostars (https://www.biostars.org/) Q and A forum for questions about bioinformatic tasks like alignment, differential expression analysis, etc., organized in a vaguely stack overflow like way.

Other place to get suggestions and padding for your Git repo would be to look at questions on boards like BioStars or StackExchange Implement, test, push, and comment with your solution. Make sure you all follow proper coding conventions too. Folks not only want the right answer they want to understand how it's done

also consider posting bioinformatics questions over at https://www.biostars.org/ instead of reddit

In the bioinformatics sphere there is this MIT-licensed Stack Exchange clone: https://github.com/ialbert/biostar-central

Note that conda sra-tools does not support ARM (M chips use customized ARM architecture ) yet and the official repo also does not provide pre-compiled version for arm. You should be able to compile it from the source but YMMV. Similarly, STAR does not officially support ARM either but compilation on your own always worths a try.

According to this, the disk space required should be about 17 times the size of the accession (for both output files and tmp files). As can be seen below, I have >500GB of disk space. Yet, I receive this output:

Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To...

Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available)

Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice):

If you are okay with looking at already processed data, chdck out https://dee2.io/. Otherwise there is https://github.com/ncbi/sra-tools for getting fastq files (a cli tool) or https://github.com/saketkc/pysradb (python)

Fasterq-dump also doesnt play nice sometimes. By that I mean it causes problems like this https://github.com/ncbi/sra-tools/issues/383

In this case, you're missing software. Specifically, you're missing sra-tools. Fortunately, this is provided via Homebrew as sratoolkit. After installing that formula, you should be able to use the prefetch command.

Yeah, unfortunately this required key entry is by design for some reason (see more here https://github.com/ncbi/sra-tools/issues/291).