Daniel:Notebook/Haplotyping/DataMap: Difference between revisions

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>Djacobse
>Djacobse
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  | chamber**_pgp1_21.BQSR.realigned.bam
  | chamber**_pgp1_21.BQSR.realigned.bam


|- style="font-size:12pt"  valign="bottom"
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | bam files-contigs
| height="15" | bam files-contigs
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs
  | chamber**.contigs.bam
  | chamber**.contigs.bam


|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
|- style="font-size:12pt"  valign="bottom"
| height="15" | bam files-by chrom
| height="15" | bam files-by chrom
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/bams_by_chromosome
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/bams_by_chromosome
  | chr*/chr*.chamber**.bam
  | chr*/chr*.chamber**.bam


|- style="font-size:12pt"  valign="bottom"
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | HAIRS-raw
| height="15" | HAIRS-raw
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS
  | chr*/fragments.chr*.chamber**.txt
  | chr*/fragments.chr*.chamber**.txt


|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
|- style="font-size:12pt"  valign="bottom"
| height="15" | HAIRS-merge
| height="15" | HAIRS-merge
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS
  | chr*/fragments.chr*.pgp1_21.txt
  | chr*/fragments.chr*.pgp1_21.txt


|- style="font-size:12pt"  valign="bottom"
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | haplotypes
| height="15" | haplotypes
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/haplotypes
  | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/haplotypes
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'''Notes:'''
'''Notes:'''

Revision as of 17:51, 21 November 2014

Data Map

Back to Notebook

This page contains the data map for the haplotyping project, specifically tables that outline locations of each of the data types.

Hi-C Data

File Type System Path File(s)
VCF TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/snps/ pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3.vcf
VCF-by chromosome TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/snps/ chr*/sorted.chr*.pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3_clean_final.vcf
bam files-original TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c PGP1.Rep1.rg.nodup.final_PE_sort.bam
bam files-by chrom TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c chr*/PGP1.final.chr*.corrected.bam
HAIRS-raw TSCC /oasis/tscc/scratch/djacobse/haplotypeSeqData/HAIRS fragments.chr*.hic.txt
HAIRS-merge XXXX XXXX XXXX
haplotypes TSCC /oasis/tscc/scratch/djacobse/haplotypeSeqData/hapcut_results haplotype.chr*.hic.txt

Notes:

  • * chromosomes 1 to 22

Bacterial Artificial Chromosome (BAC) Data

File Type System Path File(s)
VCF-All Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/filtered_vcf pgp1_variants_bac_all.Indx73to96.vcf
VCF-by chromosome XXXX XXXX XXXX
bam files-original Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/fixed.bam PGP1_***BacPool_Indx**.fixed.bam
bam files-contigs Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs Indx**.bacs.bam
bam files-by chrom Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome chr*/chr*.Indx**.bam
HAIRS-raw Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS chr*/chr*.Indx**.bam
HAIRS-merge Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS chr*/fragments.chr*.bac.txt
haplotypes Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/haplotypes haplotype.chr*.bac.txt

Notes:

  • * chromosomes 1 to 22
  • ** indexes 73 to 96
  • *** 3 or 6, some 6 pools (85 and 92) also have a **.2.fixed.bam notation

SISSOR DATA

PGP1-21

File Type-PGP1_21 Path File(s)
VCF-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber chamber**/chamber**_pgp1_21.snps.raw.vcf
VCF-pgp1_21 /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber pgp1.22.SISSOR.vcf
bam files-original /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber chamber**_pgp1_21.BQSR.realigned.bam
bam files-contigs /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs chamber**.contigs.bam
bam files-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/bams_by_chromosome chr*/chr*.chamber**.bam
HAIRS-raw /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS chr*/fragments.chr*.chamber**.txt
HAIRS-merge /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS chr*/fragments.chr*.pgp1_21.txt
haplotypes /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/haplotypes haplotype.chr*.sissor.txt

Notes:

  • * chromosomes 1 to 22
  • ** chambers 1 to 24

PGP1-22

Notes:

  • * chromosomes 1 to 22
  • ** chambers 1 to 24

Merge-SISSOR