I was working with RagTag to correct and scaffold the genome of a plant species based on the reference. Everything works just fine; however, I wish to generate contact maps with juicertools.
The first step requires a BIN/BAM which for YaSH, at least the BIN, is a standard output file — for RagTag I'm using the BAM alignment from Hi-C to the assembly I'm scaffolding, the AGP which also RagTag outputs as file format, and a FAI index which is the one for the reference genome.
Everything seems to work properly but then the TXT file in output from the command below is empty...
juicer pre -a -o $d/${ID}_${HAP}_JBAT ${ID}.${HAP}.bam $d/${ID}_${HAP}_ragtag-2/ragtag.scaffold.agp ../INLUP_amiga.fa.fai > $d/${ID}_${HAP}_JBAT.log 2>&1
Does anyone have any recommendation, or experience, in working with the combination of these two tools so that I can figure out what is going wrong? Also, there seems to be not many issues on this on the juicer Git page but if helpful I will ask there, too.
Hi there,
I was working with
RagTagto correct and scaffold the genome of a plant species based on the reference. Everything works just fine; however, I wish to generate contact maps withjuicertools.The first step requires a BIN/BAM which for
YaSH, at least the BIN, is a standard output file — forRagTagI'm using the BAM alignment from Hi-C to the assembly I'm scaffolding, the AGP which alsoRagTagoutputs as file format, and a FAI index which is the one for the reference genome.Everything seems to work properly but then the TXT file in output from the command below is empty...
Does anyone have any recommendation, or experience, in working with the combination of these two tools so that I can figure out what is going wrong? Also, there seems to be not many issues on this on the
juicerGit page but if helpful I will ask there, too.