Daniel:Notebook/Haplotyping/SISSORPipeline/2014-12-2: Difference between revisions

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#convert the bam format to sam format
#convert the bam format to sam format
#[[Media:Varbin.50k.sam.txt|Baslan et al segmentation script]]
#[[Media:Varbin.50k.sam.txt|Baslan et al segmentation script]]
##
#Output from (2) is a .txt file; the fourth column is the read count information
#Self explanatory, but requires manual isolation of column 4
#Convert readcounts to a binary present/not present format (2/1). Threshold is 20 reads/bin. Uses excel function.
#Self explanatory, requires saving as a .csv
#Self explanatory, requires repeat of (1)-(6) for each of 24 chambers
#Load [http://cran.r-project.org/web/packages/mhsmm/index.html mhsmm package] in R
#CSV file is loaded in as a vector (1s and 2s, 1x50000)
#Check the size is correct (verification)
#

Revision as of 02:15, 3 December 2014

Analyzing Eric's Algorithm

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Eric's Original Algorithm

The purpose of today is to understand the steps in Eric's algorithm at a high level. I may, in the future, wish to edit the algorithm itself (unlikely) or simply port it to a more friendly analysis pipeline, since the current pipeline requires a decent amount of excel copy/pasting. Ideally, it should be run with a single script.

Algorithm Decomposition

Note: The decomposition uses the same numbering as Eric's original algorithm (i.e. step 1 is my analysis of his step 1)

  1. convert the bam format to sam format
  2. Baslan et al segmentation script
  3. Output from (2) is a .txt file; the fourth column is the read count information
  4. Self explanatory, but requires manual isolation of column 4
  5. Convert readcounts to a binary present/not present format (2/1). Threshold is 20 reads/bin. Uses excel function.
  6. Self explanatory, requires saving as a .csv
  7. Self explanatory, requires repeat of (1)-(6) for each of 24 chambers
  8. Load mhsmm package in R
  9. CSV file is loaded in as a vector (1s and 2s, 1x50000)
  10. Check the size is correct (verification)