Hi I am looking to use kSNP4 using raw read data. I have been able to use short reads that I mapped to a reference, called variants on, generated a consensus seqeunce and used that as the input for kSNP4 and it worked very well. However, I want to use the raw short read data now to compare the results and see if I can obtain a similar tree without the bias of the reference. I know the first step to using this tool is to MakeKSNP4infile but I wanted to know if it made sense to include both read sets per sample (sample1_r1.fasta and sample1_r2.fasta) as individual inputs or to merge the two sets together to generate one sample1.fasta input?
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Hi I am looking to use kSNP4 using raw read data. I have been able to use short reads that I mapped to a reference, called variants on, generated a consensus seqeunce and used that as the input for kSNP4 and it worked very well. However, I want to use the raw short read data now to compare the results and see if I can obtain a similar tree without the bias of the reference. I know the first step to using this tool is to MakeKSNP4infile but I wanted to know if it made sense to include both read sets per sample (sample1_r1.fasta and sample1_r2.fasta) as individual inputs or to merge the two sets together to generate one sample1.fasta input?