Daniel:Notebook/Haplotyping/BACData: Difference between revisions
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>Djacobse (Created page with "=BAC Data Processing= Back to Notebook This page describes the data processing for the BAC data in the haplotyping project. For data location...") |
>Djacobse |
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#Split the BAC Contigs by chromosome | #Split the BAC Contigs by chromosome | ||
##HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index | ##HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index | ||
##Script | ##[[Media:Bam_2_bam.sh|Script]] | ||
#Extract HAIRS | #Extract HAIRS | ||
##HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome | ##HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome | ||
## | ##[[Media:Extracthairs_bychrom.sh|Script]] |
Latest revision as of 20:56, 8 December 2015
BAC Data Processing[edit]
This page describes the data processing for the BAC data in the haplotyping project. For data locations, visit the Data Map.
Processing[edit]
- samtools targetcut
- Uses read depth from the data to assign reads into contigs
- Script
- Split the BAC Contigs by chromosome
- HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index
- Script
- Extract HAIRS
- HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome
- Script