different alignment based insert size and tapestation fragmentation size
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2.4 years ago
eli_bayat ▴ 90

Hello, I am analyzing human gDNA sample in which fragmentation enhancer was used at 1X ratio. Read length is 2X151, dual index 10bp. I trimmed adapters and ran bwa mem alignment on this sample. The mean insert size was ~130 bp. However, when I talked to the lab scientist, I was told based on the tapestation fragment trace was ~800 bp and after removing adapters it should be around 600bp.

I did whatever I could to the best of my knowledge to see what caused this discrepancy, from not trimming data and ran alignment to remove reads with mapq<30, results didn't change. I cannot figure out what caused this significant difference. Any help will be appreciated.

Thanks

fragmentation_size bwa-mem_alignment insert_size tapestation_fragmentation_trace • 416 views
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