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!== | ||
* 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? -- Irwin Jungreis | * 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? -- Irwin Jungreis | ||
** 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) | |||
* 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? -- Irwin Jungreis | * 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? -- Irwin Jungreis | ||
** 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? -- Irwin Jungreis | * The FASTQ files have nucleotides in both upper and lower case. Does the difference indicate anything about that position? -- Irwin Jungreis | ||
** 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) | |||
* Your question. | * Your question. | ||
Revision as of 20:58, 18 December 2008
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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? -- Irwin Jungreis
- 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". --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? -- Irwin Jungreis
- 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? -- Irwin Jungreis
- Yes. Lower case indicates poor coverage. The assembly is done with Maq and default options. --AWZ 22:58, 18 December 2008 (EST)
- Your question.
