Hi all,
I have small RNA sequence data for 5 treatment groups with 4 replicates each. For each replicate, I want to filter the read lists to only include those sequence found at least once in each replicate. In other words, if the sequence has a count of 0 in one replicate, it should be removed from every replicate in that treatment.
Does anyone know how I could do this filter? Maybe there is a way in R using DESeq or genefilter? Or any other way? The lists are too long (1-2 million reads) to perform this in excel.
Thanks,
Claire
I have small RNA sequence data for 5 treatment groups with 4 replicates each. For each replicate, I want to filter the read lists to only include those sequence found at least once in each replicate. In other words, if the sequence has a count of 0 in one replicate, it should be removed from every replicate in that treatment.
Does anyone know how I could do this filter? Maybe there is a way in R using DESeq or genefilter? Or any other way? The lists are too long (1-2 million reads) to perform this in excel.
Thanks,
Claire
Comment