Soft-clippings in mapping

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Eric Londin

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Feb 17, 2020, 9:05:53 PM2/17/20

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Hi,

I am mapping and add in the flag '--alignEndsType EndToEnd', this should prevent any soft-clippings of the reads. Yet, as I am seeing that the majority of my reads are still being 'soft-clipped'. Am I misunderstanding the flag, or meaning of soft-clippings?

Thanks

Alexander Dobin

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Feb 26, 2020, 10:18:43 AM2/26/20

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Hi Eric,

--alignEndsType EndToEnd should disallow all soft-clipping. Please send me the Log.out file and top few lines of your SAM file that contain the reads with soft-clipping.

Cheers

Alex

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