Athurva Gore/2009-4-7: Difference between revisions

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>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...)
 
>Ajgore
(Removing all content from page)
 
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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

Latest revision as of 20:10, 7 April 2009