User Tools

Site Tools


lecture_notes:04-09-2010

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
lecture_notes:04-09-2010 [2010/04/11 22:29]
learithe
lecture_notes:04-09-2010 [2010/04/11 22:32]
learithe
Line 7: Line 7:
 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.
lecture_notes/04-09-2010.txt · Last modified: 2010/04/12 21:37 by cbrumbau