Talk:PersonalGenomes@Home

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Have questions about the project or the data? Please ask them here!)
Line 7: Line 7:
==Have questions about the project or the data? Please ask them here!==
==Have questions about the project or the data? Please ask them here!==
-
Hi:
+
* your question.
-
I'm wondering about the exon data that are currently here:
+
===From PGP4===
-
http://www.personalgenomes.org/data/PGP9.3/
+
I'm wondering about the exon data that are currently here: http://www.personalgenomes.org/data/PGP9.3/
 +
* A little bit about the format/quality of these data can be found in the [http://www.personalgenomes.org/data/PGP9.3/README.txt README]. --[[User:Alexander Wait Zaranek|AWZ]] 15:19, 13 April 2009 (EDT)
How does one read a .bed file? Ia there any point in a lay person even attempting to do this?  
How does one read a .bed file? Ia there any point in a lay person even attempting to do this?  
 +
* A bioinformatician might upload a bed file to [http://genome.ucsc.edu/cgi-bin/hgCustom?hgsid=130026527&clade=(null)&org=Human&db=hg18&hgct_do_add=1 UCSC] by cutting and pasting the URL of the bed file eg. http://www.personalgenomes.org/data/PGP9.3/004/hg18pgp4.bed.gz into the dialog box at UCSC.  You can then use the genome browser to do various things such as explore conversation of variants in other organisms or to browse various annotations.  It might be too much trouble for a lay person but this is a great question! --[[User:Alexander Wait Zaranek|AWZ]] 15:19, 13 April 2009 (EDT)     
Can you say anything about the status of the Trait-o-matic?  
Can you say anything about the status of the Trait-o-matic?  
 +
* This should be available soon.  One area of concern is that Trait-O-Matic can make variants--that are actually sequencing errors--seem to be clinically important.  We are continuing to refine the process by which variants are "called" from the underlying data.  Prior to taking any clinical action we expect participants to confirm variants in a CLIA approved laboratory.  We'd also like to avoid the, unnecessary, worry of seeing sequencing errors in a "Trait-o-matic" report.  --[[User:Alexander Wait Zaranek|AWZ]] 15:19, 13 April 2009 (EDT) 
Thanks as always,
Thanks as always,
Misha
Misha
aka PGP4
aka PGP4
 +
 +
==Older questions and answers==
==Older questions and answers==

Revision as of 15:19, 13 April 2009

Image:PGP_template4.jpg

About        Projects        Publications        PersonalGenomes@Home        Public Data        FAQ        Updates (12/23)



Contents

Have questions about the project or the data? Please ask them here!

  • your question.

From PGP4

I'm wondering about the exon data that are currently here: http://www.personalgenomes.org/data/PGP9.3/

  • A little bit about the format/quality of these data can be found in the README. --AWZ 15:19, 13 April 2009 (EDT)

How does one read a .bed file? Ia there any point in a lay person even attempting to do this?

  • A bioinformatician might upload a bed file to UCSC by cutting and pasting the URL of the bed file eg. http://www.personalgenomes.org/data/PGP9.3/004/hg18pgp4.bed.gz into the dialog box at UCSC. You can then use the genome browser to do various things such as explore conversation of variants in other organisms or to browse various annotations. It might be too much trouble for a lay person but this is a great question! --AWZ 15:19, 13 April 2009 (EDT)

Can you say anything about the status of the Trait-o-matic?

  • This should be available soon. One area of concern is that Trait-O-Matic can make variants--that are actually sequencing errors--seem to be clinically important. We are continuing to refine the process by which variants are "called" from the underlying data. Prior to taking any clinical action we expect participants to confirm variants in a CLIA approved laboratory. We'd also like to avoid the, unnecessary, worry of seeing sequencing errors in a "Trait-o-matic" report. --AWZ 15:19, 13 April 2009 (EDT)

Thanks as always, Misha aka PGP4


Older questions and answers

  • It is my understanding that the FASTQ files posted on the PGP web site contain reads from 55000 short exons, length 40-140. Could someone please provide an ordered list of the exons that are included? --IJ 0:30, 12 December 2008 (EST)
    • This web-page has a new "assembly" for PGP2 with coordinates for each capture region included. Please keep in mind that insertions and deletions are not present in the "assemblies". I have added a link to insertions and deletions at PersonalGenomes@Home#PGP2_Sample_Data --AWZ 22:58, 18 December 2008 (EST)
  • The FASTQ files include dinucleotide codes (like Y). Is that an indication that the particular individual is heterozygous at that locus and has both nucleotides? --IJ 0:30, 12 December 2008 (EST)
    • Yes. These are standard IUPAC codes. --AWZ 22:58, 18 December 2008 (EST)
  • The FASTQ files have nucleotides in both upper and lower case. Does the difference indicate anything about that position? --IJ 0:30, 12 December 2008 (EST)
    • Yes. Lower case indicates poor coverage. The assembly is done with Maq and default options. --AWZ 22:58, 18 December 2008 (EST)
  • Where can I find the PGP2 sequence data read by Swift? I only find the Illumina version here. --Jehyuk Lee 16:46, 23 December 2008 (EST)

Cleanup

  • It would be great if the above questions/answers could be incorporated into the main page. Maybe somebody could start an FAQ section? --AWZ 08:49, 20 December 2008 (EST)
Personal tools