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We recommend cleaning up projects as well as removing library files that you do not need, then removing the orphaned files. You can also export analyzed projects and save them on an external machine, then when you need them again you can import them to the server. Please see this information for more details related to: Project management, Removing library files, and Orphaned files. Right click on the data node to delete files from projects that are not needed (e.g. fastqs from project pipelines that are analyzed).

How do I add

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library files if I am not studying human or mouse?

Find the reference genome and annotation files for the species of interest using Ensembl. When adding an assembly, we will need both the reference genome and the transcriptome information library files. For more details on adding a reference genome please click here. The annotation file will give us information on gene (transcript) location and we recommend using the .gtf file format; for more information click here. We add a new assembly, click on Settings> Library files. From the Assembly drop-down list, select Add assembly. Specify a species, if you can't find the species name in the list, choose Other, type in species name and assembly version (you might have multiple assembly versions on one species, e.g. hg19 and hg38 assembly version on Homo Sapiens. You need to add reference file which is a .fasta file containing sequence information. Once the reference file is add, you can build any aligner index to perform alignment task. 

Annotation model is a file containing feature location, this file is used e.g. quantify to annotation model in RNA-seq analysis, or annotate variant or peaks in DNA-seq or ATAC-seq/ChIP-seq data analysis pipeline. The file format should be .gtf/.gff/.bed.

We recommend look for the files of the species on Ensembl website. There is no need to unzip or save these files to your local machine, instead right click and copy the link address . We also have a short video hereof the specific file (not a link to a folder). For more details, here is the documentation chapter: Library File Management - Partek® Documentation. 

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