Jwindler/AutoHiC

Could you mind giving a detailed, step-by-step pipeline for onehic.py?

aijigekoukou-shen opened this issue · 1 comments

Hi.

Thank you very much for developing the software. I generated the bam file using chromap, but I get an error when using matlock. Here is my command line. Can you give a detailed tutorial on using onehic? I got results using the example data and had so many problems using my own data. Thank you very much.

##index
samtools faidx hifi_ONT_hifiasm.hap1_final_assembly.fa
chromap -i -r hifi_ONT_hifiasm.hap1_final_assembly.fa -o hap1.index

##mapping
chromap --preset hic -r hifi_ONT_hifiasm.hap1_final_assembly.fa -x hap1.index --remove-pcr-duplicates -1 P32_R1.clean.fq.gz -2 P32_R2.clean.fq.gz --SAM -o hap1.sam -t 50

##sort
samtools view -bh hap1.sam | samtools sort -@ 50 -n > hap1.bam
rm hap1.sam 

##.assembly
python ~/biosoft/juicebox_scripts/juicebox_scripts/makeAgpFromFasta.py hifi_ONT_hifiasm.hap1_final_assembly.fa out.agp
python ~/biosoft/juicebox_scripts/juicebox_scripts/agp2assembly.py out.agp out.assembly

##.hic
conda activate morehic
matlock bam2 juicer hap1.bam out.links.txt 

INFO: converting bam to juicer on hap1.bam
INFO: detected bam filetype
INFO: reading file "hap1.bam"
FATAL: something went wrong in process_pair

remapping