I have unstranded RNA-seq data. But when I set the strand-filter one --strand-filter 1, sites are filtered because they fail. What is strand-filter doing to my data and would you recommend turning it on or off?
Also I have run mpileup separately on individual bam files. Should I run varscan mpileup2snp on each mpileup file or pileup2snp?
Thanks
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Hi,
I have unstranded RNA-seq data. But when I set the strand-filter one --strand-filter 1, sites are filtered because they fail. What is strand-filter doing to my data and would you recommend turning it on or off?
Also I have run mpileup separately on individual bam files. Should I run varscan mpileup2snp on each mpileup file or pileup2snp?
Thanks