Daniel:Notebook/Haplotyping/HiCBAC: Difference between revisions
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>Djacobse (Created page with "=Combining Hi-C and BAC Data= The purpose of this section is to go over the combining of Hi-C and BAC data to generate more accurate haplotypes. The majority of this project...") |
>Djacobse |
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**Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs | **Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs | ||
**Script: [[Media:Targetcut.txt|/media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs/targetcut.sh]] | **Script: [[Media:Targetcut.txt|/media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs/targetcut.sh]] | ||
* | *'''Chromosome Shredder''' on each index for each chromosome. Hapcut is run on each chromosome separately, and I need to keep indexes separate until the end as well. Therefore, I break up each index bam file by chromosome, and store them in separate folders (by chromosome). | ||
**Input path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs | |||
**Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome | |||
**Script: [[Media:Nai_chromosomeShredder.txt|/media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome/nai_chromosomeShredder.sh]] | |||
*'''Bam2Bam'''. The BAC data uses chromosome labeling of '1','2','3',etc., but the Hi-C data uses chromosome labeling 'chr1','chr2','chr3',etc. Hapcut, and other programs, are not clever enough to realize these are the same chromosomes. So this step inserts a 'chr' before every chromosome in the bam file. | |||
**Input path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome | |||
**Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/edit_bams_by_chromosome | |||
**Script: [[Media:Bam_2_bam.txt|/media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/edit_bams_by_chromosome/bam_2_bam.sh]] | |||
===Hi-C Data=== | |||
This data was obtained from Bing Ren's lab, and was processed by Anthony Schmitt according to their pipeline for Hi-C data. When I received the data, we already had vcfs and the final bam file. | |||
*'''Extract HAIRS''' | |||
==Combining the Data== | ==Combining the Data== |
Revision as of 21:56, 21 January 2015
Combining Hi-C and BAC Data
The purpose of this section is to go over the combining of Hi-C and BAC data to generate more accurate haplotypes. The majority of this project was done on TSCC, mostly from 11/2014-1/2015.
Pipeline
BAC Data
The BAC data is divided in to 26 indexes (numbered 73-96, with an 85.2 and a 92.2). Since 85.2 and 92.2 may be duplicates, I included both as separate samples. If they are redundant with 85 and 92 it should not harm anything.
- samtools targetcut on each index. This generates a sam file where each read is actually a contig, and may span >100kbp. For the sequence string, any reads that are implied (i.e. there is not an explicit read from the run that contains the sequence) are replaced by Ns. The final output is a bam
- Input path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/fixed.bam
- Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs
- Script: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs/targetcut.sh
- Chromosome Shredder on each index for each chromosome. Hapcut is run on each chromosome separately, and I need to keep indexes separate until the end as well. Therefore, I break up each index bam file by chromosome, and store them in separate folders (by chromosome).
- Input path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs
- Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome
- Script: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome/nai_chromosomeShredder.sh
- Bam2Bam. The BAC data uses chromosome labeling of '1','2','3',etc., but the Hi-C data uses chromosome labeling 'chr1','chr2','chr3',etc. Hapcut, and other programs, are not clever enough to realize these are the same chromosomes. So this step inserts a 'chr' before every chromosome in the bam file.
- Input path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome
- Output path: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/edit_bams_by_chromosome
- Script: /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/edit_bams_by_chromosome/bam_2_bam.sh
Hi-C Data
This data was obtained from Bing Ren's lab, and was processed by Anthony Schmitt according to their pipeline for Hi-C data. When I received the data, we already had vcfs and the final bam file.
- Extract HAIRS