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
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)
- convert the bam format to sam format
- 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 mhsmm package in R
- CSV file is loaded in as a vector (1s and 2s, 1x50000)
- Check the size is correct (verification)