Jie Huang
Dear Prof. Yu: Thanks for your nice software. For your new paper "**clusterProfiler 4.0: A universal enrichment tool for interpreting omics data**" published this year, is the full documentation on...
Hi, there: I used snp-sites to generate a VCF file for ~2 million SARS-COV-2 genome FASTA file that I downloaded from GISAID. Below is the first record:  I also...
Dear Andrew: Can I use snp-sites to process the full FASTA data that I downloaded from GISAID, which has about 1,000,000,000 lines in total for ~2 million SARS-COV-2 genomes? I...
Hi, there: I was following the online instruction to download MTAG, but got the following error. I tried to both python2 and python 3. Neither works.  Can someone please...
Hi, Guys: these days, GWAS files have up to 20 million rows, really very inefficient to query and process, if stored simply as a TXT file. I think the VCF...
Dear Peter and guys: Previously I mentioend that it is a pity (not necessarily a bug) that Pheweb could not find rsIDs for SNPs simply because their A1/A2 alleles are...
Dear Peter: Please see the error message below. I tried to run "pip3 install pheweb" on a remote server, which has python2 as default (it does have python3 installed). ...
Dear Peter and guys: 1. I think these days most GWAS don’t have REF and ALT that “must match reference genome” (required by pheweb). Also, I think in the long...
Hi, guys: I encountered the error message when running LOFTEE: **WARNING: Failed to instantiate plugin LoF: Cannot read /vep/loftee/GERP_scores.final.sorted.txt.gz using tabix at /mnt/d/software_lin/loftee/LoF.pm line 139** I found that quite many...
Hi, I am trying to run loftee on Linux. Below is my command and error message. Can someone please kindly let me know what is wrong here? Thank you &...