w9
commented
6 years ago Hi Fuwen,
Thanks for using Granatum! Single-cell RNA-Seq data typically have lots of genes that are not expressed at all across all cells. These genes sometimes take up up to 90% of the total number of genes. They provide no information for downstream analyses and can drastically slow down the computation.
I suggest you to filter out the genes before uploading it to Granatum. Were the data generated using 10x Genomics sequencing technology? In that case we recommend removing all genes that are expressed in fewer than 5% of the cells.
Also, because the limited resource on our free server, for large datasets like this we recommend you to set up your own local instance of Granatum. (Check out the "DIY" section on the front-page)
Update 05/29/2018 : The Granatum server is down for maintenance at the moment, it will be back online in a few hours.
Let me know if you have further questions!
Xun Zhu Lead developer of Granatum
Dear Author, 1 I firstly used the "TSCAN", howerver, it may take a long time to "read in " the data (10000genes, 3000cells), do you know how long it will take? 2 How long will the the "Granatum" take when I analysis my data(10000genes, 3000cells)? THANKS 之前跑TSCAN的时候感觉读数据要很长时间，我不知道我的方法对不对，大概需要多长时间呢？ granatum 分析 需要多长时间呢？ 谢谢！