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New From PGP4
It's me again. Can you please update me on the status of the PGP-10 cells and tissues? I know our lymphoblastoid cell lines are available from Coriell. What's going on with skin fibroblasts, saliva, etc.? Have those cell lines been created and if so, are they freely available to the research community?
Thanks as always,
Reply to the question on cell lines
PGP4 primary fibroblasts are currently being reprogrammed into iPS cells. They will be fully characterized in 2-3 weeks. Skin fibroblasts have been deposited at Coriell, and iPS cells will be available through Coriell soon. We expect that the request for these cell lines will increase as we make their availability widely known through multiple publications through our group and our collaborators.
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 conservation 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?
Thanks as always,
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)
- 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)