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Hi,
I am counting the total read count generated from Sequencer and aligned read count from novoalign. I counted the total read count by using wc -l -w with qseq files. I counted only single end reads. I mean I treated the paired read as one read. And I counted the aligned read by using GATK's CountReads, However, the aligned read count is larger than total read count. The GATK's CountReads count the paired read into seperate read? If then, the aligned read count is larger than total read count. I think I can divide the aligned read count by 2. If anyone has similar experience, can you tell me about this? Thank you.
I am counting the total read count generated from Sequencer and aligned read count from novoalign. I counted the total read count by using wc -l -w with qseq files. I counted only single end reads. I mean I treated the paired read as one read. And I counted the aligned read by using GATK's CountReads, However, the aligned read count is larger than total read count. The GATK's CountReads count the paired read into seperate read? If then, the aligned read count is larger than total read count. I think I can divide the aligned read count by 2. If anyone has similar experience, can you tell me about this? Thank you.