Issue in tutorial with fastq-dump -DQ option

[ChristianKKelley]

In the tutorial (http://3dgenomes.github.io/TADbit/tutorial/tutorial_1-Retrieve_published_HiC_datasets.html), is the command fastq-dump -A SRR5344921 -DQ '+' --defline-seq '@$ac.$si' -X 100000000 --split-files --outdir FASTQs/

But the -DQ option doesn't seem to be in fastq-dump anymore (at least, the -D option). Is there any update how to replicate this command in the latest fastq-dump?

[david-castillo]

Hi,

That option was gone from fastq-dump. If I remember correctly it just place a '+' in the third line of each read, but that seems the standard anyway so you can safely ignore it and do like:

fastq-dump SRR5344921 --defline-seq '@$ac.$si' -X 100000000 --split-files --outdir FASTQs/

I'll update the tutorial page.

David