Athurva Gore/2009-4-7
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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