Dear, I have a problem in Miseq data. I have paired 2x150bp reads. I have identified some false positive (repetitive in different samples) due to short mapped reads. In fastq files (both R1 and R2) I have the reads complete, but sometimes only little fragments (about 35bp) of reads from R2.fastq map to genome, as PCR duplicates .
The related reads in always in *R2.fastq, and if I look into bam file this is "Second in pair".
Anyone has any idea? Is it an experimental problem or a bioinformatic one?
Thanks
The related reads in always in *R2.fastq, and if I look into bam file this is "Second in pair".
Anyone has any idea? Is it an experimental problem or a bioinformatic one?
Thanks
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