Daniel:Notebook/Haplotyping/DataMap: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
>Djacobse
Line 6: Line 6:


==Hi-C Data==
==Hi-C Data==
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#8DB4E2;font-size:12pt;font-weight:bold"
| width="204" height="46" | File Type
| width="204" | System
| width="404" | Path
| width="589" | File(s)
|- style="font-size:12pt"  valign="bottom"
| height="15" | VCF
| TSCC
| /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/snps/
| pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3.vcf
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | 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
|- style="font-size:12pt"  valign="bottom"
| height="15" | bam files-original
| TSCC
| /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c
| PGP1.Rep1.rg.nodup.final_PE_sort.bam
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | bam files-by chrom
| TSCC
| /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c
| chr*/PGP1.final.chr*.corrected.bam
|- style="font-size:12pt"  valign="bottom"
| height="15" | HAIRS-raw
| TSCC
| /oasis/tscc/scratch/djacobse/haplotypeSeqData/HAIRS
| fragments.chr*.hic.txt
|- style="background-color:#D9D9D9;font-size:12pt"  valign="bottom"
| height="15" | HAIRS-merge
| XXXX
| XXXX
| XXXX
|- style="font-size:12pt"  valign="bottom"
| height="15" | haplotypes
| TSCC
| /oasis/tscc/scratch/djacobse/haplotypeSeqData/hapcut_results
| haplotype.chr*.hic.txt
|}


==Bacterial Artificial Chromosome (BAC) Data==
==Bacterial Artificial Chromosome (BAC) Data==

Revision as of 17:37, 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

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