Daniel:Notebook/Haplotyping

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Revision as of 01:13, 15 July 2014 by >Djacobse (→‎BAC Data)
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Haplotyping Project

Back to Notebook

Experiment List

<calendar> name=Daniel:Notebook/Haplotyping format=%name/%year-%month-%day date=2014/02/01 view=oneyear </calendar>

Data

This project utilizes several data sources. The data sources and relevant information are listed below.

BAC Data

The BAC data is on genome miner, in the following path:

  • /media/LTS_33T/KZ_LTS33T/PGP1_BacPool

The folder contains several subfolders:

  • old_calls
    • Contains the old variant call files
  • vcf_files
    • Contains a lot of vcf files
  • all_pools_combined
    • Contains all the heterozygous call files. Still unsure of the format
  • fixed.bam
    • Contains all of the bam files for each index
  • filtered_vcf
    • Seems to contain the newest .vcf files, probably the best ones to use
  • assembled_haplotypes
    • Contains the final phase output of HapCUT that was used for the BAC pools
  • het_sites
    • Contains the heterozygous site files for each chromosome. Still unsure of the format

HiC Data

The HiC data is on TSCC, in the following path:

  • /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c

Microfluidic Data

The data sets are on genome miner, in the following paths:

  • Better one:/media/Syn_15T/Eric_15T/PGP1_21
  • Second best:/media/Syn_15T/Eric_15T/PGP1_22