Talk:PersonalGenomes@Home: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
| Line 4: | Line 4: | ||
==Have questions about the project or the data? Please ask them here!== | ==Have questions about the project or the data? Please ask them here!== | ||
* 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) | * 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". --[[User:Alexander Wait Zaranek|AWZ]] 22:58, 18 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) | * 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) | ||
| Line 13: | Line 13: | ||
* Your question. | * Your question. | ||
==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) | |||
Revision as of 06:49, 20 December 2008
Don't have an account on OpenWetWare? Please join here.
Have questions about the project or the data? Please ask them here!
- 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)
- Your question.
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)
