Result_visual3-3.pl ERROR about vicaller HOT 6 OPEN

Hi JY,

Did you have "${sample}_sf.fuq" file after your running VIcaller? Can you show me the list of files you currently have?

Best,
Xun

from vicaller.

Hi, xunchen

After run VIcaller, 3 files with suffix 'fuq': ${sample}_1.1fuq, ${sample}_2.1fuq, ${sample}_1sf.fuq.
I try to step by step run, and found the file ${sample}_sf.fuq is not exist.

from vicaller.

Hi, xunchen,
VIcaller generate files as below show(by time):
sample_pe.bam
sample_soft.fastq.gz
sample_h1.sort.bam
sample_h1_1.1fq
sample_h1_2.1fq
sample_h1_h.bam
sample_su.bam
sample_sm.bam
sample_h1_pe.bam
sample_h1_soft.fastq.gz
sample_h1_h1.sort.bam
sample_1sf.fastq
IlluQC_Filtered_files
sample_1.1fq
sample_2.1fq
sample_vsu.sort.bam
sample_vsoft_sort.bam
sample.type
sample_In.virus_v3
sample_1.1fuq
sample_2.1fuq
sample_1sf.fuq
sample_1sf.othu
sample.3
sample.error
sample_f2
sample.virus_f
sample.virus_f2
sample.visualization
sample.fine_mapped
sample_vector.sam
sample_vector.hmap
sample_vector.hunmapped
sample_vector_sf.sam
sample_vector_sf.hmap
sample_vector_sf.hunmapped
sample_vector.hmapped
sample.output

Thanks a lot
JY

from vicaller.

Hi JY,

Thanks for pointing it out. The file name in the script should be changed to "1sf.fuq". It will only impact the read visualization but not viral integrations detection.

I have revised the corresponding script.

Thanks,
Xun

from vicaller.

Hi xunchen,

Thank you for your reply and help.
I have another question about virus genome. For HBV integration detection, can I just take HBV genome as virus reference?
Simply extract information of HBV reference NC_003977.1 from files virus_db_090217.fa, virus_db_090217.taxonomy and virus_db_090217.virus_list as a custom reference.

Best,
JY

from vicaller.

Yes if you change the viral database and taxonomy information consistently.

Best,
Xun

from vicaller.