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Re: PSSD Genome Project [Megathread]

Unread postPosted: Tue Sep 04, 2018 3:01 pm
by Ghost
Yes! Thanks!

Note: SNPs updated after most recent analysis.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Wed Sep 05, 2018 9:44 am
by Ciprofloxacin
I've seen your mail.

https://drive.google.com/open?id=1mOcGxW1cM21TwU8OdhojkkU0hGeZj-RQ


-You can choose the minimum number of people that must be have searched genome.
- It shows estimated remaining time on 20th attempt. Margin of error is %10-20.

No, it's no problem while all the files has same row and column types.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 06, 2018 3:18 am
by DrugsAreBad
Have you guys looked at this? I don't understand it but it looks relevant.
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

http://zzz.bwh.harvard.edu/plink/index.shtml

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 06, 2018 4:27 am
by Ciprofloxacin
Thanks to DrugsAreBad, noticed a bug in the program. It wasn't calculating SNPs which more than 10 letter. I changed the link in my prevous post. You can either restart or just use this file to complete lack SNPs.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 06, 2018 5:29 pm
by Ciprofloxacin
Ghost, these are some of SNPs of the AKR1Cx genes. If program find one of them, can you look up first it?

Rs2904804
Rs387906751
Rs387906750
Rs797044460
Rs1691053
Rs1937845
Rs2854964
Rs17134592
Rs17134585
Rs1832007
Rs7083869
Rs398122815
Rs2518049
Rs10508293
Rs12529
Rs2606345
Rs2198843
Rs162555
Rs7517566
Rs2228099
Rs10012
Rs1051740
Rs1056836
Rs1131341
Rs1799814
Rs1800440
Rs2234922
Rs2260863
Rs2066853
Rs2333227

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 06, 2018 7:11 pm
by Ghost
Yes, I've run them through the genomes.

At 50% difference limit - NO significant SNPs.

At 30% difference limit - NO significant SNPs.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 12:27 am
by Ciprofloxacin
Ghost wrote:Yes, I've run them through the genomes.

At 50% difference limit - NO significant SNPs.

At 30% difference limit - NO significant SNPs.


Could you also give raw output of these genomes at %0 limit?
Also, unfortunately noticed that, I forgot to convert capital R letters to lowercase r.
Program don't detect capital letters.

rs2904804
rs387906751
rs387906750
rs797044460
rs1691053
rs1937845
rs2854964
rs17134592
rs17134585
rs1832007
rs7083869
rs398122815
rs2518049
rs10508293
rs12529
rs2606345
rs2198843
rs162555
rs7517566
rs2228099
rs10012
rs1051740
rs1056836
rs1131341
rs1799814
rs1800440
rs2234922
rs2260863
rs2066853
rs2333227



Edit ----

I created a gene list of alpha-7-nicotinic receptors found on snpedia. I found that this receptor both related to parkinson disease and GABA inhibition. Of course, SSRI potently antagonize it.

I added a script in to the zip to extracting SNPs from plain copy of page if you want to use it. As far as program runs with only one core, you can run different searchs without any effect on performance. You know, it just uses different core.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 3:35 am
by DrugsAreBad
It seems there set of rsid:s in the pssd and control datasets are quite different. Any idea why this is? It seems more often than not that its the pssd datset that lacks information on rsids.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 1:20 pm
by DrugsAreBad
I've done some more digging around in the dataset. Here is a list of the top 25 rsids I've found that are different between the groups. What now?

rs4871622
rs1467809
rs11994900
rs6887352
rs7113273
rs9294483
rs231023
rs231024
rs2894113
rs4552410
rs7173365
rs10884674
rs2253372
rs2939402
rs588765
rs6555885
rs680244
rs12138053
rs1264704
rs1927393
rs4728731
rs6419647
rs6677662
i6058149
rs10449236

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 4:00 pm
by Ghost
Ciprofloxacin wrote:
Ghost wrote:Yes, I've run them through the genomes.

At 50% difference limit - NO significant SNPs.

At 30% difference limit - NO significant SNPs.


Could you also give raw output of these genomes at %0 limit?
Also, unfortunately noticed that, I forgot to convert capital R letters to lowercase r.
Program don't detect capital letters.

rs2904804
rs387906751
rs387906750
rs797044460
rs1691053
rs1937845
rs2854964
rs17134592
rs17134585
rs1832007
rs7083869
rs398122815
rs2518049
rs10508293
rs12529
rs2606345
rs2198843
rs162555
rs7517566
rs2228099
rs10012
rs1051740
rs1056836
rs1131341
rs1799814
rs1800440
rs2234922
rs2260863
rs2066853
rs2333227



Edit ----

I created a gene list of alpha-7-nicotinic receptors found on snpedia. I found that this receptor both related to parkinson disease and GABA inhibition. Of course, SSRI potently antagonize it.

I added a script in to the zip to extracting SNPs from plain copy of page if you want to use it. As far as program runs with only one core, you can run different searchs without any effect on performance. You know, it just uses different core.


Yea I can do that for you, I'll run it right now.
Luckily i noticed the R vs r thing yesterday and just found/replaced all in text edit.