But got this error:
Output prefix: intergeneric_allsam
Start reading the methylation file
Even cytosine sites with 0 read covered was outputted so we are going to use the total row numbers for CG (CHG/CHH) as Denominator
Use of uninitialized value in multiplication (*) at /media/khadidiatou/Transcend/all/ViewBS/lib/Meth/Coverage.pm line 114.
Illegal division by zero at /media/khadidiatou/Transcend/all/ViewBS/lib/Meth/Coverage.pm line 114.
Hello
Thank you for this tool. I've run the pipeline exactly the same as it's suggested with bismark output and with this command line
/media/khadidiatou/Transcend/all/ViewBS/ViewBS MethCoverage --reference /mnt/0616f2d5-970e-477f-bce6-bc388b441f97/home/khadidiatou/Bureau/BS_SEQ/X204SC22111727-Z01-F001/01.RawData/genome_citre/CITRE_only_9_chrom.fasta --sample Baches_rep1.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,MicroC1 --sample Baches_rep2.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,MicroC2 --sample Baches_rep3.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,MicroC3 --sample /media/khadidiatou/Transcend/result_01_bismark/HYB/Hybride_rep1.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,Hyb1 --sample /media/khadidiatou/Transcend/result_01_bismark/HYB/Hybride_rep2.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,Hyb2 --sample /media/khadidiatou/Transcend/result_01_bismark/HYB/Hybride_rep3.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,Hyb3 --sample /media/khadidiatou/Transcend/result_01_bismark/Fortune/Fortune_rep1.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,For1 --sample /media/khadidiatou/Transcend/result_01_bismark/Fortune/Fortune_rep2.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,For2 --sample /media/khadidiatou/Transcend/result_01_bismark/Fortune/Fortune_rep3.cytosine_report.txt.CpG_report.merged_CpG_evidence.cov.gz,For3 --outdir /home/khadidiatou/Bureau/ViewBS/methCoverage --prefix intergeneric_allsam
But got this error: Output prefix: intergeneric_allsam Start reading the methylation file Even cytosine sites with 0 read covered was outputted so we are going to use the total row numbers for CG (CHG/CHH) as Denominator Use of uninitialized value in multiplication (*) at /media/khadidiatou/Transcend/all/ViewBS/lib/Meth/Coverage.pm line 114. Illegal division by zero at /media/khadidiatou/Transcend/all/ViewBS/lib/Meth/Coverage.pm line 114.