Hi Dear Li,
i am trying to use PAG pipeline.
i am confuse about bed files.
if i am using 1 reference gene, then i have need to add 1 bed file of the reference genome.?
rbsa.py --type mcscan --A_bed arabidopsis.bed --B_Bed --anchor hifias-arabidopsis-anchor --scf hifiasm.fasta
for --B_bed which bed i have need to use.
i got the bed file from the hifiasm output "hifiasm.asm.bp.p_ctg.lowQ.bed". i have need to use this bed file here.?
if i use
rbsa.py --type nucmer --ref arabidopsis.fasta --scf hifiasm.fasta
i have no need to use any bed file.?
Hi Dear Li, i am trying to use PAG pipeline. i am confuse about bed files. if i am using 1 reference gene, then i have need to add 1 bed file of the reference genome.? rbsa.py --type mcscan --A_bed arabidopsis.bed --B_Bed --anchor hifias-arabidopsis-anchor --scf hifiasm.fasta for --B_bed which bed i have need to use. i got the bed file from the hifiasm output "hifiasm.asm.bp.p_ctg.lowQ.bed". i have need to use this bed file here.? if i use rbsa.py --type nucmer --ref arabidopsis.fasta --scf hifiasm.fasta i have no need to use any bed file.?
please reply me. Thanks