Hi,
I saw the minimum resouce recommended for local processing. Is there a way for me to estimate how much resource I might need my own data? maybe based on the numebr of genes identified? number of panelists involved? the size of hte file?
I want to purchase a new workstation for analyses, but I dont know what computer resource I am looking for.
Thank you!
It is unclear what you would like to do. If you mean RNAseq analysis, a modern laptop / workstation (32G RAM / 8 CPU cores) should be sufficient. If you are a Mac user, please keep in mind that some of the algorithms are not working well on the latest Apple silicon chips. The Intel / AMD chips are safer for common bioinformatics workflows at the moment
Hi Professor Xia,
Sorry, I was not very clear with my first post. Let me explain with more details.
I am currently using a Mac with M3, it does not work with the raw data processing (FASTQ files → expression table). I want to buy a new laptop to acoomodate for the raw data processing + RNAseq Analysis. In the future, I will also use the same laptop for metabolomics and microbiomics.
By using the example in protocol ( *18 sub-sampled FASTQ files from double-crested cormorant), I was able to process through online processing within 3 min. But I am not sure how long would it take for my own dataset. That is why I am curious about how do you estimate the resource you might need based on raw data file?
Based on your reply above, does it mean if I can start with intensity/counts table, 32 RAM/ 8 CPU cores would be enough? and if I need to do raw data processing, I need more resource?
Thanks!
My estimate is for raw RNAseq reads processing based on our protocol. The time for your own dataset will be related to the sequencing depth (i.e. size of the file). In general, it is ~10 min per sample in our testing using kallisto. This is the only step I suggest to do it locally - uploading the raw data to our server is very time consuming (several hours). Once you have the table, you can use our web server for analysis - all you need is a modern web browser, as computing is on our server.