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This page contains the data map for the haplotyping project, specifically tables that outline locations of each of the data types. | This page contains the data map for the haplotyping project, specifically tables that outline locations of each of the data types. | ||
==Reference Data== | |||
The reference data is the data used to create the "true" VCFs, since HAPCUT requires a true vcf file as input which informs it where the relevant sites are. The original PGP1 data is in genome miner in the directory /home/kunzhang/genomeSeq/Data/PGP1_CGI_WGS. The data was from 3 different cell lines. | |||
===Processing Reference Data=== | |||
The reference data information can be found [[Daniel:Notebook/Haplotyping/MergeVCF|here]] | |||
===Data Update Dec. 2015=== | |||
It occurs to me this needs to be better updated, so I'm linking to a google doc. | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- font-size:12pt;font-weight:bold" | |||
| width="600" height="46" | Data Map | |||
| width="600" | Notebook Link | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=0 Hi-C Data Map] | |||
| | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1124859722 BAC Data Map] | |||
| [[Daniel:Notebook/Haplotyping/BACData|Processing BAC Data]] | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1059932227 LFR Data Map] | |||
| [[Daniel:Notebook/Haplotyping/LFRData|Processing LFR Data]] | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=11247187 BAC+Hi-C Data Map] | |||
| [[Daniel:Notebook/Haplotyping/BAC-HiC|BAC and Hi-C Data Processing]] | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=2147175569 LFR + Hi-C Data Map] | |||
| [[Daniel:Notebook/Haplotyping/LFR-HiC|LFR and Hi-C Data Processing]] | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=676014356 BAC+Hi-C+LFR Data Map] | |||
| [[Daniel:Notebook/Haplotyping/LFR-BAC-HiC|LFR+BAC+Hi-C Data Processing]] | |||
|- style="font-size:12pt" valign="bottom" | |||
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1920656431 BEAGLE Data Map] | |||
| [[Daniel:Notebook/Haplotyping/BEAGLE|BEAGLE Data Processing]] | |||
|} | |||
==Hi-C Data== | ==Hi-C Data== | ||
Line 89: | Line 136: | ||
| PGP1_***BacPool_Indx**.fixed.bam | | PGP1_***BacPool_Indx**.fixed.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 | ||
| Genome Miner | | Genome Miner | ||
Line 95: | Line 142: | ||
| Indx**.bacs.bam | | Indx**.bacs.bam | ||
|- style=" | |- style="font-size:12pt" valign="bottom" | ||
| height="15" | bam files-by chrom | | height="15" | bam files-by chrom | ||
| Genome Miner | | Genome Miner | ||
Line 101: | Line 148: | ||
| chr*/chr*.Indx**.bam | | chr*/chr*.Indx**.bam | ||
|- style="font-size:12pt" valign="bottom" | |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | ||
| height="15" | HAIRS-raw | | height="15" | HAIRS-raw | ||
| Genome Miner | | Genome Miner | ||
Line 107: | Line 154: | ||
| chr*/chr*.Indx**.bam | | chr*/chr*.Indx**.bam | ||
|- style=" | |- style="font-size:12pt" valign="bottom" | ||
| height="15" | HAIRS-merge | | height="15" | HAIRS-merge | ||
| Genome Miner | | Genome Miner | ||
Line 113: | Line 160: | ||
| chr*/fragments.chr*.bac.txt | | chr*/fragments.chr*.bac.txt | ||
|- style="font-size:12pt" valign="bottom" | |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | ||
| height="15" | haplotypes | | height="15" | haplotypes | ||
| Genome Miner | | Genome Miner | ||
Line 131: | Line 178: | ||
===PGP1-21=== | ===PGP1-21=== | ||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#D8E4BC;font-size:12pt;font-weight:bold" | |||
| width="159" height="56" | File Type-PGP1_21 | |||
| width="545" | Path | |||
| width="433" | File(s) | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | VCF-by chrom | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber | |||
| chamber**/chamber**_pgp1_21.snps.raw.vcf | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | VCF-pgp1_21 | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber | |||
| pgp1.22.SISSOR.vcf | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | bam files-original | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber | |||
| chamber**_pgp1_21.BQSR.realigned.bam | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | bam files-contigs | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs | |||
| chamber**.contigs.bam | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | bam files-by chrom | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/bams_by_chromosome | |||
| chr*/chr*.chamber**.bam | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | HAIRS-raw | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS | |||
| chr*/fragments.chr*.chamber**.txt | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | HAIRS-merge | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS | |||
| chr*/fragments.chr*.pgp1_21.txt | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | haplotypes | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/haplotypes | |||
| haplotype.chr*.sissor.txt | |||
|} | |||
'''Notes:''' | '''Notes:''' | ||
Line 140: | Line 233: | ||
===PGP1-22=== | ===PGP1-22=== | ||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#D8E4BC;font-size:12pt;font-weight:bold" | |||
| width="159" height="38" | File Type-PGP1_22 | |||
| width="545" | Path | |||
| width="433" | File(s) | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | VCF-by chrom | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | |||
| chamber**/pgp22_chamber**.snps.raw.vcf | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | VCF-pgp1_22 | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | |||
| pgp1.22.SISSOR.vcf | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | bam files-original | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | |||
| chamber**/pgp22_chamber*.BQSR.realigned.bam | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | bam files-contigs | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs | |||
| chamber**.contigs.bam | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | bam files-by chrom | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/bams_by_chromosome | |||
| chr*/chr*.chamber*.bam | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | HAIRS-raw | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS | |||
| chr*/fragments.chr*.chamber*.txt | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | HAIRS-merge | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS | |||
| chr*/fragments.chr*.pgp1_21.txt | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | haplotypes | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/haplotypes | |||
| haplotype.chr*.sissor.txt | |||
|} | |||
'''Notes:''' | '''Notes:''' | ||
Line 148: | Line 287: | ||
===Merge-SISSOR=== | ===Merge-SISSOR=== | ||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#D8E4BC;font-size:12pt;font-weight:bold" | |||
| width="159" height="36" | File Type-SISSOR (PGP1-21,22) | |||
| width="545" | Path | |||
| width="433" | File(s) | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | VCF-PGP1 | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22 | |||
| pgp1_21and22.vcf | |||
|- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | |||
| height="15" | HAIRS-merge | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/HAIRS | |||
| fragments.chr*.sissor.txt | |||
|- style="font-size:12pt" valign="bottom" | |||
| height="15" | haplotypes | |||
| /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/haplotypes | |||
| haplotype.chr*.sissor.txt | |||
|} | |||
'''Notes:''' | |||
* * chromosomes 1 to 22 |
Latest revision as of 18:11, 15 December 2015
Data Map[edit]
This page contains the data map for the haplotyping project, specifically tables that outline locations of each of the data types.
Reference Data[edit]
The reference data is the data used to create the "true" VCFs, since HAPCUT requires a true vcf file as input which informs it where the relevant sites are. The original PGP1 data is in genome miner in the directory /home/kunzhang/genomeSeq/Data/PGP1_CGI_WGS. The data was from 3 different cell lines.
Processing Reference Data[edit]
The reference data information can be found here
Data Update Dec. 2015[edit]
It occurs to me this needs to be better updated, so I'm linking to a google doc.
Hi-C Data[edit]
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[edit]
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[edit]
PGP1-21[edit]
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[edit]
File Type-PGP1_22 | Path | File(s) |
VCF-by chrom | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | chamber**/pgp22_chamber**.snps.raw.vcf |
VCF-pgp1_22 | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | pgp1.22.SISSOR.vcf |
bam files-original | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber | chamber**/pgp22_chamber*.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/pgp22/bams_by_chromosome | chr*/chr*.chamber*.bam |
HAIRS-raw | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS | chr*/fragments.chr*.chamber*.txt |
HAIRS-merge | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS | chr*/fragments.chr*.pgp1_21.txt |
haplotypes | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/haplotypes | haplotype.chr*.sissor.txt |
Notes:
- * chromosomes 1 to 22
- ** chambers 1 to 24
Merge-SISSOR[edit]
File Type-SISSOR (PGP1-21,22) | Path | File(s) |
VCF-PGP1 | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22 | pgp1_21and22.vcf |
HAIRS-merge | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/HAIRS | fragments.chr*.sissor.txt |
haplotypes | /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/haplotypes | haplotype.chr*.sissor.txt |
Notes:
- * chromosomes 1 to 22