Dinh/Dinh 2015/NOTES/2015-1-7: Difference between revisions

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>Dinh
(Created page with "= 141216_HiSeqRapidRun = * Processed files are copied to genome-miner at: /media/Ext12T/DD_Ext12T/MONOD/141216_HiSeqRapidRunWGBS ** Sub-directories: BAMfiles, MethylFreq, BEDf...")
 
>Dinh
mNo edit summary
 
(11 intermediate revisions by the same user not shown)
Line 3: Line 3:
** Sub-directories: BAMfiles, MethylFreq, BEDfiles
** Sub-directories: BAMfiles, MethylFreq, BEDfiles
* Library information from Noi: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-25
* Library information from Noi: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-25
* Perform trimming with '''trim-galore''' and mapping with '''bwa mem'''
* 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)
** 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
* Use tscc with 4 processors per node
===Mapping steps===
===Mapping steps===
* Make a table:
* Make a table:
  PC-P_2 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq   s_1_1_ILMN_Indx01.txt,s_1_2_ILMN_Indx01.txt     64     none   AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC     AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT     WGBS
{| class="wikitable"
  PC-P_4 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq   s_1_1_ILMN_Indx03.txt,s_1_2_ILMN_Indx03.txt     64     none   AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC     AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT     WGBS  
| PC-P_2||150106_HiSeqRapidWGBS/Fastq||s_1_1_ILMN_Indx01.txt,s_1_2_ILMN_Indx01.txt||64||none||AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC||AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT||WGBS
  NC-7   /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq   s_1_1_ILMN_Indx07.txt,s_1_2_ILMN_Indx07.txt     64     none   AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC     AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT     WGBS
|-
  PC-P_9  /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq   s_1_1_ILMN_Indx08.txt,s_1_2_ILMN_Indx08.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
  6-P-1   /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq   s_1_1_ILMN_Indx09.txt,s_1_2_ILMN_Indx09.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 table file into 27 files, 1 line/sample per file:
   split -l 1 list_my_files aa_
   split -l 1 list_my_files aa_
* Run Go.Map.sh script on tscc, each sample will be processed on a separate node.
* 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
  <nowiki>#===Change the following paths===#
  <nowiki>#===Change the following paths===#
cur_dir=`pwd`
cur_dir=`pwd`
Line 105: Line 157:
| PCT-7_map|| 7,697,260 || 15,394,520 || 15,030,202 || 12,980,554 ||2%||86%
| PCT-7_map|| 7,697,260 || 15,394,520 || 15,030,202 || 12,980,554 ||2%||86%
|}
|}
===SNP matrix===
* 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 | 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