How to manage the 267 GB for RNA seq analysis

1

Dear Galaxy Support Team,

I am currently using Galaxy for RNA-seq analysis as part of a wheat rust resistance gene cloning project. My research involves EMS-induced susceptible mutants and resistant wild-type lines, and I plan to perform differential expression analysis and SNP discovery from RNA-seq data.

I noticed that my current Galaxy storage quota is approximately 268 GB. Given the size of wheat RNA-seq datasets and the number of samples involved, I am concerned that this quota may not be sufficient to complete the analysis.

Could you please advise on the best practices for managing storage efficiently within Galaxy? Specifically, I would appreciate guidance on:
Whether intermediate files can be safely deleted after each analysis step.

  1. Which file types typically consume the most storage (FASTQ, BAM, count matrices, etc.).
  2. Recommended strategies for handling approximately 10 RNA-seq samples.
  3. Whether additional storage can be requested for academic research projects.
  4. Any workflow recommendations that minimize disk usage during RNA-seq analysis.

My project focuses on identifying candidate genes underlying wheat leaf rust resistance through EMS mutagenesis and RNA-seq-based variant analysis.

Thank you for your assistance.
Kind regards,

2

Hi @Innocent_Kwaku_Dorvl,

Consider doing data analysis in batches and upload only data required for immediate analysis. Once you are at the read counts table step, the storage requirements are minimal. At this step you can delete raw data (reads) and big intermediate files (trimmed reads, alignments). Make sure you complete all relevant QC before deleting the data. After that proceed with analysis of next batch. Use compressed formats over ASCII based (fastqsanger.gz datatype in Galaxy, not fastqsanger).

Make sure you purge deleted datasets. Unpurged data counts towards the user quota.

In my experience, RNA-Seq analysis requires 3-5x more storage for intermediate data than the raw data, depending on protocol.

Some servers provide a short term access for big quota. You may try this option, as well.

Hope that helps.

Kind regards,

Igor

3

Thank you very much! I am going to consider this detailed explanation.

Best regards.