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Old 02-21-2018, 03:40 AM   #7
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Location: Cambridge

Join Date: Sep 2010
Posts: 115
Lightbulb Try having a look at thumbnails or raw images.

In this case first try having a look at the raw thumbnail/image data, and make a movie from the run's tiles (using imagemagic, one frame per cycle).

This can help a lot in understanding what actually is going on.
Usually the read quality is better with lower cluster densities on the Miseq/Hiseq2500/NextSeq instruments.

Also it is a good idea to capture the raw images when working with ancient DNA.
(So they can be reprocessed later).

In case of MiSeq it would mean doing some storage mods: attaching an external DAS array and mounting is as drive D: Ideally you want to use esata type one set in RAID 10 like 8-16TB of useable capacity and make sure to use 64KB clusters for NTFS volume or use IFSD driver with ext4 and large allocate.
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