Editing
Daniel:Notebook/Haplotyping/DataMap
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
=Data Map= [[Daniel:Notebook/Haplotyping|Back to Notebook]] 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== {| 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 |} '''Notes:''' * * chromosomes 1 to 22 ==Bacterial Artificial Chromosome (BAC) Data== {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="background-color:#E6B8B7;font-size:12pt;font-weight:bold" | width="128" height="35" | File Type | width="117" | System | width="452" | Path | width="294" | File(s) |- style="font-size:12pt" valign="bottom" | height="15" | VCF-All | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/filtered_vcf | pgp1_variants_bac_all.Indx73to96.vcf |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | height="15" | VCF-by chromosome | XXXX | XXXX | XXXX |- style="font-size:12pt" valign="bottom" | height="15" | bam files-original | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/fixed.bam | PGP1_***BacPool_Indx**.fixed.bam |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | height="15" | bam files-contigs | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs | Indx**.bacs.bam |- style="font-size:12pt" valign="bottom" | height="15" | bam files-by chrom | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome | chr*/chr*.Indx**.bam |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | height="15" | HAIRS-raw | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS | chr*/chr*.Indx**.bam |- style="font-size:12pt" valign="bottom" | height="15" | HAIRS-merge | Genome Miner | /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS | chr*/fragments.chr*.bac.txt |- style="background-color:#D9D9D9;font-size:12pt" valign="bottom" | height="15" | 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=== {| 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:''' * * chromosomes 1 to 22 * ** chambers 1 to 24 ===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:''' * * chromosomes 1 to 22 * ** chambers 1 to 24 ===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
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information