Dinh/Dinh 2015/NOTES/2015-1-7: Difference between revisions
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(5 intermediate revisions by the same user not shown) | |||
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===Mapping steps=== | ===Mapping steps=== | ||
* Make a table: | * Make a table: | ||
{| | {| class="wikitable" | ||
| PC-P_2|| | | PC-P_2||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx01.txt,s_1_2_ILMN_Indx01.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PC-P_4|| | | PC-P_4||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx03.txt,s_1_2_ILMN_Indx03.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| NC-7|| | | NC-7||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx07.txt,s_1_2_ILMN_Indx07.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PC-P_9|| | | PC-P_9||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx08.txt,s_1_2_ILMN_Indx08.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6-P-1|| | | 6-P-1||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx09.txt,s_1_2_ILMN_Indx09.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6-P-2|| | | 6-P-2||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx10.txt,s_1_2_ILMN_Indx10.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6-P-3|| | | 6-P-3||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx11.txt,s_1_2_ILMN_Indx11.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-3|| | | 7-P-3||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx20.txt,s_1_2_ILMN_Indx20.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-5|| | | 7-P-5||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx21.txt,s_1_2_ILMN_Indx21.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-6|| | | 7-P-6||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx22.txt,s_1_2_ILMN_Indx22.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-7|| | | 7-P-7||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx23.txt,s_1_2_ILMN_Indx23.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-8|| | | 7-P-8||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx25.txt,s_1_2_ILMN_Indx25.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7-P-10|| | | 7-P-10||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx27.txt,s_1_2_ILMN_Indx27.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6T-1|| | | 6T-1||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx04.txt,s_2_2_Indx04.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6T-2|| | | 6T-2||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx05.txt,s_2_2_Indx05.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6T-3|| | | 6T-3||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx06.txt,s_2_2_Indx06.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6T-4|| | | 6T-4||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx07.txt,s_2_2_Indx07.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 6T-5|| | | 6T-5||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx08.txt,s_2_2_Indx08.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7T-1|| | | 7T-1||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx09.txt,s_2_2_Indx09.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7T-2|| | | 7T-2||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx10.txt,s_2_2_Indx10.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7T-4|| | | 7T-4||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx12.txt,s_2_2_Indx12.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| 7T-5|| | | 7T-5||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx13.txt,s_2_2_Indx13.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PCT-1|| | | PCT-1||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx14.txt,s_2_2_Indx14.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PCT-2|| | | PCT-2||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx15.txt,s_2_2_Indx15.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PCT-4|| | | PCT-4||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx16.txt,s_2_2_Indx16.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PCT-6|| | | PCT-6||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx17.txt,s_2_2_Indx17.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|- | |- | ||
| PCT-7|| | | PCT-7||150106_HiSeqRapidWGBS/Fastq||s_2_1_Indx18.txt,s_2_2_Indx18.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS | ||
|} | |} | ||
* Split table file into 27 files, 1 line/sample per file: | * Split table file into 27 files, 1 line/sample per file: | ||
Line 165: | Line 165: | ||
/home/dinh/scripts/BisReadMapper/src/tped-merge.pl | /home/dinh/scripts/BisReadMapper/src/tped-merge.pl | ||
* Run plink: | * Run plink: | ||
/home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --tfile monod_141216 --recode --transpose --out monod_141216.plink | /home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --geno 0 --maf 0.01 --tfile monod_141216 --recode --transpose --out monod_141216.plink | ||
**** 92639 SNPs failed missingness test ( GENO > 0 ) | |||
**** 84830 SNPs failed frequency test ( MAF < 0.01 ) | |||
993 SNPs left. | |||
/home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --tfile monod_141216.plink --cluster --matrix | /home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --tfile monod_141216.plink --cluster --matrix | ||
* the plink.mibs fie is a N x N matrix of genome-wide average IBS pairwise identities | * the plink.mibs fie is a N x N matrix of genome-wide average IBS pairwise identities | ||
Line 175: | Line 178: | ||
dev.off() | dev.off() | ||
* SNPs dendrogram: | * SNPs dendrogram: | ||
[[File: | [[File:monod_capture_plink_mibs.png | 800px]] |
Latest revision as of 21:07, 3 February 2015
141216_HiSeqRapidRun[edit]
- Processed files are copied to genome-miner at: /media/Ext12T/DD_Ext12T/MONOD/141216_HiSeqRapidRunWGBS
- Sub-directories: BAMfiles, MethylFreq, BEDfiles
- Library information from Noi: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-25
- Perform trimming with trim-galore, mapping with bwa mem, overlapping PE are clipped with bamUtils
- For trimming, use methylated adaptors sequences, quality trim with -q 20 from 3' ends, and trim 5 bp from 5' ends (methylation bias)
- Do not remove clonal reads
- Use Hg19_lambda reference (Hg19 plus LambdaDNA fasta files).
- Use tscc with 4 processors per node
Mapping steps[edit]
- Make a table:
PC-P_2 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx01.txt,s_1_2_ILMN_Indx01.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PC-P_4 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx03.txt,s_1_2_ILMN_Indx03.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
NC-7 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx07.txt,s_1_2_ILMN_Indx07.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PC-P_9 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx08.txt,s_1_2_ILMN_Indx08.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6-P-1 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx09.txt,s_1_2_ILMN_Indx09.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6-P-2 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx10.txt,s_1_2_ILMN_Indx10.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6-P-3 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx11.txt,s_1_2_ILMN_Indx11.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-3 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx20.txt,s_1_2_ILMN_Indx20.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-5 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx21.txt,s_1_2_ILMN_Indx21.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-6 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx22.txt,s_1_2_ILMN_Indx22.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-7 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx23.txt,s_1_2_ILMN_Indx23.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-8 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx25.txt,s_1_2_ILMN_Indx25.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7-P-10 | 150106_HiSeqRapidWGBS/Fastq | s_1_1_ILMN_Indx27.txt,s_1_2_ILMN_Indx27.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6T-1 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx04.txt,s_2_2_Indx04.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6T-2 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx05.txt,s_2_2_Indx05.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6T-3 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx06.txt,s_2_2_Indx06.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6T-4 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx07.txt,s_2_2_Indx07.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
6T-5 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx08.txt,s_2_2_Indx08.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7T-1 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx09.txt,s_2_2_Indx09.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7T-2 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx10.txt,s_2_2_Indx10.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7T-4 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx12.txt,s_2_2_Indx12.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
7T-5 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx13.txt,s_2_2_Indx13.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PCT-1 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx14.txt,s_2_2_Indx14.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PCT-2 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx15.txt,s_2_2_Indx15.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PCT-4 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx16.txt,s_2_2_Indx16.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PCT-6 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx17.txt,s_2_2_Indx17.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
PCT-7 | 150106_HiSeqRapidWGBS/Fastq | s_2_1_Indx18.txt,s_2_2_Indx18.txt | 64 | none | AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT | WGBS |
- Split table file into 27 files, 1 line/sample per file:
split -l 1 list_my_files aa_
- Run Go.Map.sh script on tscc, each sample will be processed on a separate node.
- New script added to simplify BisReadMapper pipeline: MasterBisReadMapper.pl in BisReadMapper_v1.4
#===Change the following paths===# cur_dir=`pwd` scripts_dir="/home/ddiep/scripts/BisReadMapper/src" #===Begin===# for n in aa_aa aa_ap aa_ab aa_ac aa_ad aa_ae aa_af aa_ag aa_ah aa_ai aa_aj aa_ak aa_al aa_am aa_an aa_ao aa_aq aa_ar aa_as aa_at aa_au aa_av aa_aw aa_ax aa_ay aa_az aa_ba do #1) Run mapper: echo "#!/bin/csh" > $n.job echo "#PBS -l nodes=1:ppn=4" >> $n.job echo "#PBS -l walltime=14:00:00" >> $n.job echo "#PBS -o $n.log" >> $n.job echo "#PBS -e $n.err" >> $n.job echo "#PBS -V" >> $n.job echo "#PBS -M diep.hue.dinh@gmail.com" >> $n.job echo "#PBS -m abe" >> $n.job echo "#PBS -A k4zhang-group" >> $n.job echo "cd /state/partition1/\$USER/\$PBS_JOBID" >> $n.job #echo "cd $cur_dir" >> $n.job echo "$scripts_dir/MasterBisReadMapper.pl -i $cur_dir/$n -s $cur_dir/list_paths_Hg19 -b yes > $cur_dir/$n.status" >> $n.job echo "cp -r * $cur_dir/" >> $n.job qsub -q hotel $n.job done #===End===#
Mapping statistics[edit]
SAMPLE ID | Total PE reads | Total reads | Total reads after trimming | Total mapped reads | %trimmed | %mapped |
6-P-1_map | 6,304,203 | 12,608,406 | 11,953,618 | 10,355,738 | 5% | 87% |
6-P-2_map | 6,984,763 | 13,969,526 | 13,303,090 | 11,570,287 | 5% | 87% |
6-P-3_map | 7,758,987 | 15,517,974 | 14,491,124 | 12,482,525 | 7% | 86% |
6T-1_map | 7,086,511 | 14,173,022 | 13,834,798 | 11,869,709 | 2% | 86% |
6T-2_map | 7,489,616 | 14,979,232 | 14,638,550 | 12,820,323 | 2% | 88% |
6T-3_map | 23,044,384 | 46,088,768 | 45,125,296 | 36,126,640 | 2% | 80% |
6T-4_map | 7,345,257 | 14,690,514 | 14,302,984 | 12,351,984 | 3% | 86% |
6T-5_map | 8,242,846 | 16,485,692 | 16,084,486 | 13,871,915 | 2% | 86% |
7-P-10_map | 6,405,081 | 12,810,162 | 12,126,962 | 10,375,497 | 5% | 86% |
7-P-3_map | 5,117,607 | 10,235,214 | 9,714,174 | 8,343,291 | 5% | 86% |
7-P-5_map | 5,943,036 | 11,886,072 | 11,311,240 | 9,868,792 | 5% | 87% |
7-P-6_map | 8,151,067 | 16,302,134 | 15,454,040 | 13,420,765 | 5% | 87% |
7-P-7_map | 8,006,228 | 16,012,456 | 15,215,062 | 13,264,972 | 5% | 87% |
7-P-8_map | 6,321,921 | 12,643,842 | 11,948,422 | 10,309,480 | 6% | 86% |
7T-1_map | 7,397,882 | 14,795,764 | 14,414,610 | 12,579,473 | 3% | 87% |
7T-2_map | 7,913,136 | 15,826,272 | 15,471,842 | 13,386,508 | 2% | 87% |
7T-4_map | 7,428,250 | 14,856,500 | 14,495,860 | 12,632,367 | 2% | 87% |
7T-5_map | 7,933,340 | 15,866,680 | 15,474,202 | 13,465,056 | 2% | 87% |
NC-7_map | 8,140,557 | 16,281,114 | 15,329,258 | 11,685,910 | 6% | 76% |
PC-P_2_map | 6,236,300 | 12,472,600 | 11,848,168 | 10,306,946 | 5% | 87% |
PC-P_4_map | 6,400,370 | 12,800,740 | 12,191,246 | 10,561,291 | 5% | 87% |
PC-P_9_map | 7,500,258 | 15,000,516 | 14,213,460 | 12,272,000 | 5% | 86% |
PCT-1_map | 7,092,180 | 14,184,360 | 13,848,186 | 11,921,316 | 2% | 86% |
PCT-2_map | 8,566,243 | 17,132,486 | 16,739,144 | 14,465,075 | 2% | 86% |
PCT-4_map | 8,189,668 | 16,379,336 | 16,003,166 | 13,781,204 | 2% | 86% |
PCT-6_map | 9,228,450 | 18,456,900 | 17,987,752 | 15,681,405 | 3% | 87% |
PCT-7_map | 7,697,260 | 15,394,520 | 15,030,202 | 12,980,554 | 2% | 86% |
SNP matrix[edit]
- Run MasterBisReadMapper with variant calling. Since I already have the sam files to give as input, MasterBisReadMapper will not need to re-map the data.
- Homozygous SNPs are also called at dbSNP138 positions.
- After getting the *filtered.SNP.txt files, generate the tped and tfam files for plink.
/home/dinh/scripts/BisReadMapper/src/snp2tfiles.pl
- Merge tped files into the large tped matrix for plink.
/home/dinh/scripts/BisReadMapper/src/tped-merge.pl
- Run plink:
/home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --geno 0 --maf 0.01 --tfile monod_141216 --recode --transpose --out monod_141216.plink **** 92639 SNPs failed missingness test ( GENO > 0 ) **** 84830 SNPs failed frequency test ( MAF < 0.01 ) 993 SNPs left. /home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --tfile monod_141216.plink --cluster --matrix
- the plink.mibs fie is a N x N matrix of genome-wide average IBS pairwise identities
- use R to plot the dendrogram:
A = read.table("plink.mibs", F) labels = read.table("monod_141216.plink.tfam",F) colnames(A) = labels$V2 plot(hclust(as.dist(1-A)), main="plink.mibs") dev.off()
- SNPs dendrogram:
File:Monod capture plink mibs.png