MiSeq HDD Space

[cement_head]

Hello,

We have a MiSeq and so far, so good - but our HDD is now getting very full. How do I free up space? Is this done automatically, or do I need to delete the old data folders/files?

Thanks,
Andor

[dfhdfh]

Instead of deleting, I would move them to another system or, preferably, some kind of backup system.

[GenoMax]

You need to delete older data folders from the MiSeq to free up space (make sure you first make backup copies elsewhere). You can find this folder generally under D:\Illumina\MiSeqAnalysis.

[austinso]

Just to add, you just need to decide what you want to keep and backup:

1. Each run on the Miseq generates two redundant data folders D:\Illumina\MiSeqAnalysis (as pointed out by GenoMax) and D:\Illumina\MiSeqOutput. It also stores the most recent run in the D:\Illumina\MiSeqTemp folder. You can backup either one of first two.

2. What is more important for you as far as being able to recreate your dataset...the BAM+BAI+FASTQ files, or just the FASTQ files or the original image files in the L001 directory of these folders (the hierarchy escapes me right now)? The caveat is that reanalysis involving demultiplexing requires the original image files, which can really only be done on the Miseq anyway. It is the L001 folder (the one with the TIFF files and not the LOCS) that gobbles up most of your storage.

Once you've decided on your backup strategy, then you can delete away. It is a pain to do this manually because it takes a while, so if your IT guy can set up a cron job to do this automatically to a NAS (network attached storage), that would be your best bet.

[GenoMax]

@austinso has provided a more comprehensive answer. I tend to forget about the other folder since we do not use the on-board analysis that MiSeq provides.

To extend #2 from austinso - one can do the de-multiplexing off-line by using CASAVA/bcl2fastq (requires separate install of linux software) as long as the L001 folder is available. One can presumably do the same analysis as what MiSeq does by doing a stand-alone install of MiSeq Reporter (needs a computer with better specs than a standard desktop). All this software is available from iCom (Illumina) at no cost.

[ScottC]

You can also use BaseSpace as a de facto backup if you're not already doing that, but it will only work for future runs if you start doing it now (you can't retrospectively send your data there). This probably isn't as reliable as your own, simply because it's controlled by Illumina and you can't be completely sure how long it'll persist, persist in the same format, or remain free.