On my workstation I use winzip to unpack these. I hoped to unpack these with the online tools, but none of the ziptools recognized the fq.gz files. How can I unpack these here on galaxy? Or is it possible to analyze and assemble gz.files unpacked.
Yes, you can just work with fastq.gz datasets. If you really want to uncompress the data, you can click on the dataset’s pencil icon, switch to the Convert tab and select the uncompressed format as Target datatype.
Ok, I will try that, even if the convertion option only seems to be fastocq and sanger format. I am sure I will run into an issue with that later on. I also tried to upload a previously unpacked fastq.gz, it was initially a pair of two apprx 50 gb files ( four pairs and two sanger files). After unzipping the 50gb files the files were over 250 gb each, and once one of these was uploaded to usegalaxy it split up into two 250 gb files. I am not sure where to start.
The paired files are 275, 262, 258 and 180 gb each, before upload. I have increased my quota temporarily to 2 tb for handling of the files, but I am not sure if it is feasable to upload and analyze them.
Increasing the account quota size will allow for more data storage space.
Analysis of the data is dependent on the resources allocated to cluster nodes, and the capabilities of the underlying tools you plan to use. This is all true whether using Galaxy to manage the jobs or not.
Where are you working?
From a Xeon workstation in my temporary workplace. I would like to end up with a file around 16 gb, seven chromsones and proper enough to submit to the IWGSC.
The discussions you may find at this forum (or other places) tend to focus on public computational resources (what we allocate at the “free” services) – and those limits won’t apply for you. Galaxy itself can be used for the largest of work.
So … you’ll need to scale up your compute resources to fit the analysis. The authors of the tools you plan to use likely have documentation online, or in a publication. As admin of the server you can then set the resources for any particular tool to use.
Is that what you need to know – where to configure the resources?
Ok, thank you both. I will try to look into it, hopefully I will find my way through the Galaxy service with some bases left.