Who is doing clinical sequencing here?

[Heisman]

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?

[jp.]

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

Originally Posted by Heisman

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?

[Heisman]

I haven't done RNA-seq, hopefully someone else can chime in. Why do you want 500 np inserts?

[jp.]

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 ?

Originally Posted by Heisman

I haven't done RNA-seq, hopefully someone else can chime in. Why do you want 500 np inserts?

[Heisman]

Originally Posted by jp.

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.

[jp.]

Thank you very much for your help, however, may you recommend me something on WGS?

Originally Posted by Heisman

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.

[jp.]

May you give me answer for the probblem posted here
http://seqanswers.com/forums/showthr...098#post112098

Originally Posted by Heisman

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?

[LSerhGute]

When sequencing in the CLIA lab, are you doing proprietary panels used for diagnoses? or is it all still clinical research

[yongbao1]

we do clinical sequencing

[LSerhGute]

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?

[jdmendez]

Hi, i am doing Clinical Sequencing using Illumina TruSightOne, coupled with Sophia Diagnosis platform. I am in a developing country (Panama), so the challenges are huge!!!

Looking forward to interact with other experts in Clinical Diagnosis to start interactions, colabs, and any other crazy idea!

Jorge