The clipping tool seems to generate debris

[許博程]

Hi,

I am currently apply HiC data to modify the genome assembly.

After mapping HiC data to the genome, I apply these codes to generate the file Juice box.

Here it is:

awk 'BEGIN{OFS="\t"} { scaffold_name = $1 scaffold_length = $2 print scaffold_name, "1", scaffold_length, "1", "W", scaffold_name, "1", scaffold_length, "+" }'../../00_raw_genome/Filter_contamination_Filter_N50percent_eel52_CL_LCBGF_CL_L99.fasta.fai >simple_scaffolds.agp

#produce files that juicebox requires # Note bam file from chromap (from the result of hic-scaffolding-nf) to save time

juicer pre -a -o juicebox_Nscaffolding/out_JBAT chromap/aligned.bam ../00_raw_genome/simple_scaffolds.agp ../00_raw_genome/Filter_contamination_Filter_N50percent_eel52_
CL_LCBGF_CL_L99.fasta.fai

asm_size=$(awk '{s+=$2} END{print s}'../00_raw_genome/Filter_contamination_Filter_N50percent_eel52_CL_LCBGF_CL_L99.fasta.fai)
java -Xmx36G -jar ~/tools/juicer_tools_1.22.01.jar pre juicebox_Nscaffolding/out_JBAT.txt juicebox_Nscaffolding/out_JBAT.hic <(echo "assembly ${asm_size}")

I am if these codes can affect the result or not, so I just provide here for reference.

When I try to edit with Juice box (by using shift select the scaffold and clip/click the target site), a fragment was generated from clipping. I am not sure if this is a bug or not.

I hope someone can tell if this is my wrong operation, and how to solve it. I am using MacBook Pro M2 chip laptop.

Thanks~

A debris was generated for unknown reason!