BGM

How to generate variants by RNA-seq using vg tools

2

Hi Vg team, I have a problem,I'm wondering if Vg tools can be used for variants(snp;indel;SV) call basing on bulk RNA sequencing. You known that the small variants can be...

How to deal with the Error messages using hap.py with VFC in example catalogue

1

Hi,Peter I want to compare two VCF file using hap.py, So I try to test hap.py as document described, ,But I got serval error messages like below,Can you give me...

Hi, I want to align the assembled sequence (HJ.stLFR_CCS.maternal.fasta.gz HJ.stLFR_CCS.paternal.fasta.gz) to the human HPRC reference sequence (HPRC.Phase1.CHM13v2_Non-W.gfa) using the following command. The final GFA output (out.gfa) is smaller than the...

spades-core finished abnormally, err code: 4

6

### Description of bug Dear spades team, * system call for: "['/home/users/ddu/anaconda3/pkgs/cloudspades-3.12.0-0/bin/spades-core', '/home/users/ddu/projects/009.RA/002.linked-reads/Assembly/Script/Cloudspades_HP1/K77/configs/config.info']" finished abnormally, err code: -8 Best, Du ### spades.log [spades.log.zip](https://github.com/ablab/spades/files/10068202/spades.log.zip) ### params.txt [params.txt.zip](https://github.com/ablab/spades/files/10068211/params.txt.zip) ### SPAdes version cloudspades-3.12.0...

Hi, The overall MAF file was obtained based on 10 genomes comparison, I want to find the regions that satisfy the conditions: highly similar in Sample1, Sample2, Sample3 and no...

Alignment error

4

Hi, I tried to use GraphAligner(GraphAligner -g CPC.HPRC.Phase1.CHM13v2_Non-W.gfa -f /HJ.stLFR_CCS.maternal.fasta.gz -a aln.gam -x vg), But I got several errors message.Can you give me some suggestions. 

Early stopping Abnormality

6

### System Info Copy-and-paste the text below in your GitHub issue and FILL OUT the two last points. - `transformers` version: 4.32.1 - Platform: Linux-4.18.0-372.9.1.el8_lustre.x86_64-x86_64-with-glibc2.17 - Python version: 3.11.5 -...