Pe150+8(+8?)+150

mdegraaf · 02-25-2020, 01:11 PM

Hi,
We have prepared a bunch of libraries with the Nextera Flex kit, with the use of the index plate (Nextera™ DNA CD Indexes (96 Indexes, 96 Samples). Now we are sending pooled libraries off to be sequences and we have to select if we want PE150+8+150 or PE150+8+8+150. Unfortunately there is no further information on what this means. Does anyone know? I would think the double 8 because of dual indexing but would appreciate any input

GSviral · 02-25-2020, 11:58 PM

Hello mdegraaf,

You are correct with your assumption. The PE 8 + 8 option refers to a dual indexing strategy while the PE 8 option will just be a single indexing approach. However, if you are still concerned I would advise getting in contact with the sequencing provider and they can put your mind at ease fairly quickly.

Hope this helps!

mdegraaf · 02-26-2020, 02:20 PM

Thank you for your answer. I did contact the provider but haven't heard back from them yet.

kmcarr · 02-27-2020, 09:01 AM

mdegraaf,

You didn't say how many libraries you pooled. If it is more than 12 then it is inevitable that you have more than one library sharing a common i7 index sequence. i7 is the first of the two index sequenced or the ONLY index sequenced if you choose PE150+8+150. You can not use this format if any i7 index is repeated in your pool, you must then use PE150+8+8+150. Honestly I'd always choose the dual index sequencing format; what would be the downside to it?

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02-25-2020, 01:11 PM	#1
mdegraaf Junior Member Location: Canada Join Date: Feb 2020 Posts: 5	Pe150+8(+8?)+150 Hi, We have prepared a bunch of libraries with the Nextera Flex kit, with the use of the index plate (Nextera™ DNA CD Indexes (96 Indexes, 96 Samples). Now we are sending pooled libraries off to be sequences and we have to select if we want PE150+8+150 or PE150+8+8+150. Unfortunately there is no further information on what this means. Does anyone know? I would think the double 8 because of dual indexing but would appreciate any input

02-25-2020, 11:58 PM	#2
GSviral Member Location: UK Join Date: Dec 2014 Posts: 37	Hello mdegraaf, You are correct with your assumption. The PE 8 + 8 option refers to a dual indexing strategy while the PE 8 option will just be a single indexing approach. However, if you are still concerned I would advise getting in contact with the sequencing provider and they can put your mind at ease fairly quickly. Hope this helps!

02-26-2020, 02:20 PM	#3
mdegraaf Junior Member Location: Canada Join Date: Feb 2020 Posts: 5	Thank you for your answer. I did contact the provider but haven't heard back from them yet.

02-27-2020, 09:01 AM	#4
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	mdegraaf, You didn't say how many libraries you pooled. If it is more than 12 then it is inevitable that you have more than one library sharing a common i7 index sequence. i7 is the first of the two index sequenced or the ONLY index sequenced if you choose PE150+8+150. You can not use this format if any i7 index is repeated in your pool, you must then use PE150+8+8+150. Honestly I'd always choose the dual index sequencing format; what would be the downside to it?