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Old 07-20-2015, 11:31 AM   #1
upendra_35
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Default Maximum insert size with Hiseq 3000

What is the maximum size of insert allowed/optimum in Hiseq 3000? For one of our analysis, we needed a longer insert size (~800bp) which is ok in the case of 2000 but i was told that it is not good in the case of 3000. Can anyone comment on this?
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Old 07-21-2015, 08:04 AM   #2
NextGenSeq
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Anything over 500 bp is not recommended.
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Old 07-22-2015, 06:45 AM   #3
andibody
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I heard fragments from 400bp on or even below would start causing problems?
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Old 07-22-2015, 12:30 PM   #4
luc
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Please see:
http://dnatech.genomecenter.ucdavis....data-download/
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Old 07-23-2015, 03:20 AM   #5
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If the size bias is so extreme, does it mean that applications with non-random insert sizes shouldn't be run on the HiSeq3000/4000 at all?
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Old 07-23-2015, 03:25 AM   #6
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This thread has some useful information about data characteristics from that HiSeq 3000 dataset linked above: http://seqanswers.com/forums/showthread.php?t=58353

Last edited by GenoMax; 07-23-2015 at 03:55 AM.
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Old 07-23-2015, 03:44 AM   #7
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Thanks for the link!
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