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Old 07-28-2013, 12:39 AM   #21
Heisman
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Sorry I did not respond earlier. I am confused. Why do you want to build your own reference genome? What do you mean in your last post when you say you are going for 500 reads? You seem to want to do a lot of different experiments; do you have people around you who you can further discuss this with?
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Old 07-28-2013, 04:37 AM   #22
jp.
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Thank Heisman
As I wrote earlier, I am almost a lone wolf :|
However, I have changed my plans.
Now want to detect clinically relevant Variants and might look something common between my my available RNA-seq data and thinking for 500 insert PE.
Can you please tell me your best strategies, if you were at my place ?
Thank you


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Originally Posted by Heisman View Post
Sorry I did not respond earlier. I am confused. Why do you want to build your own reference genome? What do you mean in your last post when you say you are going for 500 reads? You seem to want to do a lot of different experiments; do you have people around you who you can further discuss this with?
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Old 07-28-2013, 07:43 AM   #23
Heisman
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I haven't done RNA-seq, hopefully someone else can chime in. Why do you want 500 np inserts?
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Old 07-28-2013, 08:20 AM   #24
jp.
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because I think it will be good to detect variants and mutation. Also, I think that this much will be good enough to study SNP and gene expression.
What are your recommendations for some one who is doing WGS for the first time ?
what should one study if checking control vs treatment or normal vs diseased ?
How much should be insert and depth ?
May I know your opinion, if your guide gives you human samples (control vs treatment, and normal vs diseased) and if you are doing first time WGS ?
You may please write which may not be perfect but at least to start WGS with ?

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I haven't done RNA-seq, hopefully someone else can chime in. Why do you want 500 np inserts?
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Old 07-28-2013, 11:36 AM   #25
Heisman
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Originally Posted by jp. View Post
because I think it will be good to detect variants and mutation. Also, I think that this much will be good enough to study SNP and gene expression.
What are your recommendations for some one who is doing WGS for the first time ?
what should one study if checking control vs treatment or normal vs diseased ?
How much should be insert and depth ?
May I know your opinion, if your guide gives you human samples (control vs treatment, and normal vs diseased) and if you are doing first time WGS ?
You may please write which may not be perfect but at least to start WGS with ?
I think you should start a new thread as I definitely won't be able to help you with RNA-seq stuff. I recommend you read a few reviews on the various experiments you are considering doing so you have a better idea of everything that goes into the data analysis and how to design the experiments.
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Old 07-28-2013, 06:07 PM   #26
jp.
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Thank you very much for your help, however, may you recommend me something on WGS?

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Originally Posted by Heisman View Post
I think you should start a new thread as I definitely won't be able to help you with RNA-seq stuff. I recommend you read a few reviews on the various experiments you are considering doing so you have a better idea of everything that goes into the data analysis and how to design the experiments.
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Old 07-30-2013, 07:01 PM   #27
jp.
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May you give me answer for the probblem posted here
http://seqanswers.com/forums/showthr...098#post112098


Quote:
Originally Posted by Heisman View Post
Sorry I did not respond earlier. I am confused. Why do you want to build your own reference genome? What do you mean in your last post when you say you are going for 500 reads? You seem to want to do a lot of different experiments; do you have people around you who you can further discuss this with?
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Old 09-11-2013, 03:59 PM   #28
LSerhGute
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When sequencing in the CLIA lab, are you doing proprietary panels used for diagnoses? or is it all still clinical research
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Old 10-01-2013, 09:46 AM   #29
yongbao1
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we do clinical sequencing
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Old 10-01-2013, 02:48 PM   #30
LSerhGute
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I realize my question may not have been clear. The reason for my question was that I was hoping to learn two things:

1.When doing clinical sequencing in the CLIA lab, are you doing targeted or WGS?

2. Was the sequencing test prescribed by a Dr. to diagnose a disease, and if so, did you lab develop the test?
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