Tanger Zhang

Hi @pjx1990 We had a discuss how to generate the .hic and .assembly files. Please see this thread (https://github.com/tangerzhang/ALLHiC/issues/68). And thanks for noticing us the matplot error.

Yes, you are right! Thanks for pointing that out. I will fix it tomorrow once I can login my github account. xinghua1001 ***@***.***> 于2021年4月1日周四 下午11:30写道： > Hi Dr. Zhang, >...

Hi, I will prefer to use 40 as the quality cutoff, i.e., samtools view -bq 40 Actually, ALLHiC_pip.sh takes fastq files as input as this script will perform two rounds...

Hi @ddelgadillod When scaffolding the tetraploid sugarcane genome, I first assigned contigs into 10 homologous groups based on its close relatives, sorghum genome following this wiki guideline (https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-scaffolding-an-auto-polyploid-sugarcane-genome). After that,...

Hi @ptranvan For the question 1 and 2, the answer is yes. You can follow this pipeline to anchor a diploid genome (https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-scaffolding-of-a-simple-diploid-genome). There is no need to use a...

Hi @ptranvan The error is likely caused by incomplete bam file or contig assembly. Could you please double check your bam file and fasta contig file? Otherwise, you can paste...

Yes, it seems that the group2 is a chimeric scaffold. As far as I know, juicebox can adjust the hic scaffolding. You actually can convert ALLHiC assembly to .hic and...

It is likely the issue related to an old version of samtools. Please refer to this one: https://github.com/tangerzhang/ALLHiC/issues/1