Talk:PersonalGenomes@Home: Difference between revisions
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==Have questions about the project or the data? Please ask them here!== | ==Have questions about the project or the data? Please ask them here!== | ||
* 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? --[[User:Irwin Jungreis|IJ]] 0:30, 12 December 2008 | |||
===New From PGP4=== | |||
Hi: | |||
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, | |||
Misha (PGP4) | |||
====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. | |||
Thanks. | |||
Jay | |||
===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 [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? | |||
* 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 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! --[[User:Alexander Wait Zaranek|AWZ]] 15:19, 13 April 2009 (EDT) | |||
Can you say anything about the status of the Trait-o-matic? | |||
* About 5% of your "exomes" is analyzed here: http://snp.med.harvard.edu/samples/PGP9.3_-_04 --[[User:Alexander Wait Zaranek|AWZ]] 16:05, 28 September 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? --[[User:Irwin Jungreis|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]] --[[User:Alexander Wait Zaranek|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? --[[User:Irwin Jungreis|IJ]] 0:30, 12 December 2008 (EST) | |||
** Yes. These are standard IUPAC codes. --[[User:Alexander Wait Zaranek|AWZ]] 22:58, 18 December 2008 (EST) | ** Yes. These are standard IUPAC codes. --[[User:Alexander Wait Zaranek|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? --[[User:Irwin Jungreis|IJ]] 0:30, 12 December 2008 | * The FASTQ files have nucleotides in both upper and lower case. Does the difference indicate anything about that position? --[[User:Irwin Jungreis|IJ]] 0:30, 12 December 2008 (EST) | ||
** Yes. Lower case indicates poor coverage. The assembly is done with Maq and default options. --[[User:Alexander Wait Zaranek|AWZ]] 22:58, 18 December 2008 (EST) | ** Yes. Lower case indicates poor coverage. The assembly is done with Maq and default options. --[[User:Alexander Wait Zaranek|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. --[[User:Jehyuk Lee|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? --[[User:Alexander Wait Zaranek|AWZ]] 08:49, 20 December 2008 (EST) |
Latest revision as of 08:42, 19 October 2009
Have questions about the project or the data? Please ask them here!New From PGP4Hi: 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, Misha (PGP4) Reply to the question on cell linesPGP4 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. Thanks. Jay
From PGP4I'm wondering about the exon data that are currently here: http://www.personalgenomes.org/data/PGP9.3/
How does one read a .bed file? Ia there any point in a lay person even attempting to do this?
Can you say anything about the status of the Trait-o-matic?
Thanks as always, Misha aka PGP4 Older questions and answers
Cleanup
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