Q:
I’m trying to run FunSeq2 through the online application. I’ve tried a few times over the past few days, but always get this error message: "Sorry, but the requested page is unavailable due to a server hiccup." Can you please advise?

I am still not able to run FunSeq2 online; I’m getting the same error message as before. I also downloaded the source scripts and can run example input, however, it is extremely slow when trying to run >1,000 input SNPs (20hr+ on cluster computing). I noticed that Supplemental Table 5 says it can process 2,000 SNPs in 2 minutes – is this for the online version only?

Do you have suggestions for working with the online version? I’ve tried tab delimited .bed and a mix of double spacing for the positions and tabs for the alleles .bed (as suggested by the ARVIN method), and neither work for me.

A:
I have double-checked the webserver and done some testing, the server works as usual. But I noticed some input formatting may cause the error you had. for example, please follow the format we suggested, and use <tab> delimiter not space. If you still have problems, could you share your input file, so we can help to figure out the problem?

However, considering the webserver is based on an old version of FunSeq2, we recommend you use our latest version. We have also prepared a pre-calculated whole-genome score on hg19 and hg38(leftover). You just need to download the score and use tabix tools and bed to query. For details, please refer http://funseq2.gersteinlab.org/downloads