Hi! Thank you very much for share this nice tool!I used the gap-filling step of this tool and my command is as follows python3 /public-supool/home/marison/software/quarTeT-main/quartet_gapfiller.py -d /public-dss/share/gap_lab/Assembly/ragtag/tydm58_hifi/scaffold/ragtag.scaffold.fasta -g $contig1 $contig2 $contig3 $contig4 $contig5 $contig6 $contig7 -i 70 -f 2500 -t 20 -l 800 --overwrite. The log shows that the program worked well and finished the job.
The problem is that when I check these filled gaps in IGV at the same position of [quarTeT.genome.filled.stat] file, these filled gaps' position remains the 'N'*100.Moreover,I used a script write by myself to check the gap in [quarTeT.genome.filled.fasta] file,it seems the filled gap still remian in the filled assembly. I wonder if there are some details in command I hadn't noticed or something else lead to this result?
Hi! Thank you very much for share this nice tool!I used the gap-filling step of this tool and my command is as follows
python3 /public-supool/home/marison/software/quarTeT-main/quartet_gapfiller.py -d /public-dss/share/gap_lab/Assembly/ragtag/tydm58_hifi/scaffold/ragtag.scaffold.fasta -g $contig1 $contig2 $contig3 $contig4 $contig5 $contig6 $contig7 -i 70 -f 2500 -t 20 -l 800 --overwrite. The log shows that the program worked well and finished the job. The problem is that when I check these filled gaps in IGV at the same position of [quarTeT.genome.filled.stat] file, these filled gaps' position remains the 'N'*100.Moreover,I used a script write by myself to check the gap in [quarTeT.genome.filled.fasta] file,it seems the filled gap still remian in the filled assembly. I wonder if there are some details in command I hadn't noticed or something else lead to this result?