Forum: Bioinformatics
08-05-2019, 06:10 PM
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Replies: 3
Views: 981
Illumina output questions
Hello, I am gonna do some Illumina 2X300bp amplicon sequencing. I suppose the platform (MiSeq) will run 600 cycles and time fixed. I just recently notice on the official website
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Forum: Bioinformatics
07-12-2019, 04:49 PM
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Replies: 10
Views: 1,915
Hmm, interesting. I didn't realize MiSeq has...
Hmm, interesting. I didn't realize MiSeq has 2X150bp runs choice. Again, this is new sequencing center. My previous center for Amplicon sequencing only has 2X300bp or default is this settings. I am...
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Forum: Bioinformatics
07-12-2019, 02:06 PM
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Replies: 10
Views: 1,915
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Forum: Bioinformatics
07-12-2019, 01:56 PM
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Replies: 10
Views: 1,915
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Forum: Bioinformatics
07-12-2019, 01:54 AM
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Replies: 10
Views: 1,915
Did my sequencing center did a sloppy job?
Hello, I have just got my 16S rRNA amplicon sequencing back. We use typical Earth Microbiome Project primers 515F-806R, which is about 290bp size of amplicon.
We requested MiSeq 300bp X 2 pair-end...
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Forum: General
05-27-2019, 08:41 PM
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Replies: 6
Views: 2,310
Hi Thanks for you information. I am using a...
Hi Thanks for you information. I am using a different brand called Geneaid. However, the product comes with very simple protocol. It only says that I can clean up the DNA from 100bp to 10kb. It only...
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Forum: General
05-26-2019, 07:58 PM
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Replies: 6
Views: 2,310
Hello AvantS,
Thank you very much. Can you...
Hello AvantS,
Thank you very much. Can you give me the details (website link) of AMpure beads 1.2X. I am not sure what is 1.2 X? I heard Ampure beads XP. Are they same thing?
Thanks.
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Forum: General
05-23-2019, 04:59 PM
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Replies: 6
Views: 2,310
NGS clean up kit
Hello, I am want to purify some PCR amplicons (16S rRNA) for Illumina sequencing.
I have many samples and I did my PCR in 96-well plates. I was told the best way to do it is using magnetic beads...
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Forum: Illumina/Solexa
05-09-2019, 03:22 PM
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Replies: 5
Views: 1,908
Thanks. I just want to make sure if the...
Thanks. I just want to make sure if the sequencing primers for bridge amplification step for Illumina sequencing? Am I right? I just want to know which step the sequencing center would use these...
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Forum: Illumina/Solexa
05-09-2019, 02:06 PM
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Replies: 5
Views: 1,908
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Forum: Illumina/Solexa
05-07-2019, 06:47 PM
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Replies: 5
Views: 1,908
Basic questions about Illumina Amplicon sequecing
Hi, I've just moved to a new lab. We normally do barcoded bacterial 16S rRNA and fungal ITS sequencing. However, this new lab's protocol and primers design are quite different from my previous lab's....
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Forum: Illumina/Solexa
04-14-2019, 04:07 PM
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Replies: 1
Views: 934
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Forum: Illumina/Solexa
02-20-2019, 07:37 PM
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Replies: 5
Views: 1,150
“R1 and R2 of the fragment are in oppossite...
“R1 and R2 of the fragment are in oppossite direction". -- I know this. However, my question is when they sequence R1 and R2, do they have to use two primers? For example, R1 uses forward primer and...
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Forum: Illumina/Solexa
02-20-2019, 07:09 PM
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Replies: 5
Views: 1,150
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Forum: Illumina/Solexa
02-20-2019, 04:09 PM
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Replies: 5
Views: 1,150
MiSeq amplicon sequencing Primers?
Hi guys,
I sent some soil samples to a commercial sequencing center. I do fungal ITS sequencing (300bpX 2 paired-end) Miseq.
As you know, I use forward and reversed primers when I did PCR. I...
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Forum: General
02-20-2019, 03:53 PM
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Replies: 5
Views: 1,782
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Forum: General
02-19-2019, 01:31 PM
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Replies: 5
Views: 1,782
Hi GenoMax,
I wish I could post a pic. I...
Hi GenoMax,
I wish I could post a pic. I left my previous lab and moved to a new lab. I am setting up a new lab. I want to buy some, but I don't know the name. So, I can't google it. I have to...
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Forum: General
02-18-2019, 07:22 PM
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Replies: 5
Views: 1,782
Does anyone know the name of this PCR rack?
Hi, I moved to a new lab. My old lab has some special PCR "clamping" Rack. I want to buy some, but I can't find it online. I don't know the official name, so I can't google for it.
I can describe...
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Forum: Bioinformatics
09-06-2018, 08:37 PM
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Replies: 0
Views: 821
Some questions about KO classification
Hello, I have some questions about the KO classification.
I have a KO function abundance table. It will give me the basic level of KO funcitons ( the lowest level). Results like this:
#OTU ID...
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Forum: Illumina/Solexa
08-18-2017, 10:01 AM
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Replies: 5
Views: 2,075
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Forum: Illumina/Solexa
08-18-2017, 09:47 AM
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Replies: 5
Views: 2,075
Price of sequencer
Hello, how much is MiSeq (include service. warranty)? I saw Illumina has MiniSeq online. Has anyone used it before? How much is MiniSeq?
Ben
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Forum: Bioinformatics
08-16-2017, 11:39 AM
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Replies: 1
Views: 1,358
Should I worry about the direction of my reads
Hello, I recently got my metagenomic illumina sequencing back (hiseq). There is one sample that I would like to do some blast. Since it was sequenced using paired-end sequencing (I have two fastq...
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Forum: Bioinformatics
04-12-2017, 01:27 PM
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Replies: 1
Views: 903
What percentage should I use?
Hi, I have some results from BLASTX. If I set % of identity to 60%, I will loss more than 50% of reads (results), compare to identity cutoff to 30%.
Should I use 30%? Is there any rule of thumb?...
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Forum: Bioinformatics
04-06-2017, 05:03 PM
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Replies: 3
Views: 1,097
Can we sequence RNA directly
Hello, couple of years ago, I was in a NGS workshop. I was told some company was trying to develop some kits, so we can do metatranscriptomics without building cDNA libraries. I was wondering if this...
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Forum: Bioinformatics
03-30-2017, 11:38 AM
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Replies: 13
Views: 2,232
Hi GenoMax,
Thanks. BTW, do you know is...
Hi GenoMax,
Thanks. BTW, do you know is there any good forum to discuss R application. Bioconductor.org focus on molecular bioinformatics. I need some forums such as help people with plots...
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