Athurva Gore/2009-4-7

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Revision as of 20:08, 7 April 2009 by >Ajgore (New page: =Notes for April 7= * Met with Dr. Zhang yesterday ** Will transcribe written Notes ** Have pasted raw text file notes below LOOK AT BROAD HYBRIDIZATION SEQUENCING /Volumes/Drive2 100...)
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Notes for April 7

  • Met with Dr. Zhang yesterday
    • Will transcribe written Notes
    • Have pasted raw text file notes below
LOOK AT BROAD HYBRIDIZATION SEQUENCING

/Volumes/Drive2
1000Genome is from 1000Genome Project, can play with mapping
RefGenomes - Mouse and Drosophila Genomes

Data is under /Users/kunzhang/WorkSpace
/Users/kunzhang/WorkSpace/ExomeSeq/Solexa/03072009

FastQ Format
Kun_PGP1AC_s_1_sequence_03_07_2009.txt

4 lines together is one sequencing read
ID
Sequence
Quality Score

Mapping software can handle this kind of format
SOAP is not very good on mac
MAQ is being used
	Stored in /usr/local/bin

In human genome, 3 directory
	Hg18 is raw sequence (lowercase is repeat)
	Masked - repeats are Ns
	snp129Mask - Every SNP in DB SNP database also shows up
		Represented as a degenerate code

Repeats or SNPs after the first 12bp are allowed if absolutely necessary
	In order to have greatest amount of coverage

ExomeSeq/Dec08
	Probe design and scripts are in here
	2nd round - covers missing exons due to chr_randoms
Scripts in this folder:
FoldEnergyScriptKun.pl		primer2SQL.pl
calculate_probe_coverage.pl	primers2padlock-Dec08.pl
findRedundantExons.pl		probes2BED.pl
getMissingCcdsExon.pl		refExon2BED.pl
getMissingCcdsExonMethod2.pl	refExon2ccdsExon.pl
missingExonAnnotation.pl	refExonID2ccdsExonID.pl
mockReadGenerator.pl		toFa.pl
pickProbes.pl

Documentation is on wiki
3rd round plugs in even more gaps
98% coverage after this

Scripts are a bit messy

Two orders
	Jan 09-258k probes - still being sequenced
	Mar 09-Also included miRNA genes
		Round 2 - 16k
		Round 3 - 34k
			Round 3 might have some overlaps
			Used different primer set to easily separate
	Small probes were capturing homologous regions
		>95% identity across 70 base pairs - hard to map back to genome
		Synthesized as separate subset
		Probably more efficient