User Tools

Site Tools


lecture_notes:05-13-2011

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
lecture_notes:05-13-2011 [2011/06/12 17:43]
karplus [Insert Length Analysis] added pointer to main discussion
lecture_notes:05-13-2011 [2015/09/11 19:47]
5.9.83.211 ↷ Links adapted because of a move operation
Line 1: Line 1:
 ====== Insert Length Analysis (lecture notes) ====== ====== Insert Length Analysis (lecture notes) ======
  
-We discussed the results from mapping the Illumina run 2 reads to the 454 reads using [[bioinformatic_tools:​bwa|BWA]]. +We discussed the results from mapping the Illumina run 2 reads to the 454 reads using [[archive:bioinformatic_tools:​bwa|BWA]]. 
-There is a more complete analysis at [[bioinformatic_tools:​bwa#​determining_paired-end_insert_size|Determining Paired-end Insert Size]].+There is a more complete analysis at [[archive:bioinformatic_tools:​bwa#​determining_paired-end_insert_size|Determining Paired-end Insert Size]].
 ===== Template Length ===== ===== Template Length =====
  
Line 9: Line 9:
 First, we determined what this histogram really shows in the distribution of template lengths, the length from the leftmost base mapped to the rightmost. This size includes the length of each read in the pair and the insert region between them.  First, we determined what this histogram really shows in the distribution of template lengths, the length from the leftmost base mapped to the rightmost. This size includes the length of each read in the pair and the insert region between them. 
  
-Both these distributions show smaller template lengths than the previous estimates (see [[computer_resources:​data|computer_resources:​data]]). The distribution for barcode 8 is especially odd because it appears to be cut off at 100. The read lengths for both barcodes were around 100 bps so any template length less than 200 represents a pair that can be joined. It was decided that SeqPrep should be run prior to mapping the reads to avoid these pairs that overlap.+Both these distributions show smaller template lengths than the previous estimates (see [[archive:computer_resources:​data|computer_resources:​data]]). The distribution for barcode 8 is especially odd because it appears to be cut off at 100. The read lengths for both barcodes were around 100 bps so any template length less than 200 represents a pair that can be joined. It was decided that SeqPrep should be run prior to mapping the reads to avoid these pairs that overlap.
  
 ===== 454 Coverage ===== ===== 454 Coverage =====
lecture_notes/05-13-2011.txt · Last modified: 2015/09/11 19:47 by 5.9.83.211