JD12138
JD12138
Hi, I want to use your HGSVC graph for my own analysis. In your ftp website, I saw many different graphs. As following: 1) https://cgl.gi.ucsc.edu/data/giraffe/mapping/graphs/for-NA19240/hgsvc/hs38d1/HGSVC_hs38d1.sampled.64* 2) https://cgl.gi.ucsc.edu/data/giraffe/calling/hgsvc/ 3) https://cgl.gi.ucsc.edu/data/giraffe/products/HGSVC_hs38d1.* 4)...
Hi, I have two fastq files. I map them to a same graph and then genotype them use vg call in the same parameters. So I get two vcf files....
Hi, I have vcf files and fastq files for 80 samples. I firstly construct a vg graph with the 80 vcf files. Secondly I map the fastq to the vg...
Hello TALON group, After running your program I get this message: **ValueError: Annotation name 'aranno' not found in this database. Try one of the following:** 'aranno' is the name that...
Hello, I get the sample.call.cns file. And there are 10 columns. I don't understand the "gene" column. If there are 10 genes listed in a row with a log2Ratio of...
Hello, I have a pair of WGS sample (A normal and a tumor). And I use the command line to detect CNVs. **cnvkit.py batch $tumor --normal $normal \ --fasta $reference...
Hi, I aimed to detect novel transcript with HIFI reads using stringtie2(guided mode). Then I compare the result to gencode(v44) annotation. But almost half of the novel transcripts are marked...
Hello, I used the HPRC pangenome (https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz) to do the analysis. My processes to do the analysis are listed below. 1. build an index (**vg autoindex -g hprc-v1.0-minigraph-grch38.gfa -T ./tmp**...