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lecture_notes:04-09-2010 [2010/04/11 22:29] learithe |
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Take fix mode script from /projects/compbio/bin/scripts and replace protein user group with BME 235 user group. | Take fix mode script from /projects/compbio/bin/scripts and replace protein user group with BME 235 user group. | ||
- | Next week will have a reference genome (//Pyrobaculum oguniense//, aka "//Pog//") to use for testing the tools on. | + | Next week will have a reference genome (//Pyrobaculum oguniense//, aka //"Pog"//) to use for testing the tools on. |
- | For the most part POG is done; however, there are still some uncertainty with 8 SNPs left. It is definitely past the MIAMI standard at this point. | + | For the most part Pog is done; however, there are still some uncertainty with 8 SNPs left. It is definitely past the MIAMI standard at this point. (//Pog// assembly is down to only 8 snps & one potentially variable insert) |
- | Note about sequencing platform quality scores: most platforms are trying to use the phred quality score((http://en.wikipedia.org/wiki/Phred_quality_score)), so the quality score is comparable between the platforms and runs | + | Note about sequencing platform quality scores: most platforms are trying to use the phred quality score((http://en.wikipedia.org/wiki/Phred_quality_score)), so the quality score is theoretically comparable between the platforms and runs (although calibration causes scores to vary between runs and instruments nonetheless) |
It can be informative, once reads are mapped, to look at the quality scores for reads with observed errors. | It can be informative, once reads are mapped, to look at the quality scores for reads with observed errors. | ||
- | //Pog// assembly is down to only 8 snps & one potentially variable insert | + | |
Lior Pachter (from UC Berkeley) is vising on Monday, to speak about the Bowtie/TopHat/CuffLinks algorithms. Bowtie: mapping; TopHat/Cufflinks: find splice junctions, predicted spliced transcripts. Bowtie is used in a lot of the assembly agorithms. | Lior Pachter (from UC Berkeley) is vising on Monday, to speak about the Bowtie/TopHat/CuffLinks algorithms. Bowtie: mapping; TopHat/Cufflinks: find splice junctions, predicted spliced transcripts. Bowtie is used in a lot of the assembly agorithms. |