hechun

Hello! I want to use 3d-dna-master/lift/lift-input-annotations-to-asm-annotations.awk to map my annotation file from input onto the assembly chromosome according to a particular asm and cprops file, but I do not know...

Hi I tried to run 3d-dna/run-asm-pipeline.sh script with merged_nodups.txt generated from juicer. After it is running, appear an awk syntax error: ...visualizing round 0 results: :) -p flag was triggered....

why I can not select a scaffold with juicerbox.2.12

ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --

1

Hi, I ran multiple whole genome alignments using cactus to generate the hal file, and ran the "cactus-hal2maf js_hal2maf evolver27species.hal evolver27species.maf.gz --refGenome xxxx --chunkSize 500000" to transform the hal file....

ERROR: Intact TE annotation not found in Aros.genome.fa.mod.EDTA.intact.gff3 at EDTA.pl line 638.

2

Hi, I ran the command "perl ~/mambaforge/envs/EDTA/bin/EDTA.pl -genome Aros.genome.fa -t 56 -sensitive 1 -anno 1 --evaluate 1 --species others --force 1",but I met a problem. The error are as follows:...

make_masked.pl Permission denied

1

Hi Shujun, I want to get softmasked genome. I used this command "perl ../util/make_masked.pl -genome genome.fa -minlen 80 -hardmask 0 -t 2 -rmout genome.fa.mod.EDTA.anno/genome.fa.mod.EDTA.TEanno.out",but this error occurred "Permission denied ../util/make_masked.pl...