Rui:DNAseq analysis on HL114

From ZhangLabWiki
Revision as of 01:23, 12 March 2012 by >RuiLiu (Created page with '==Data== * Library: RL_Fib100c_29s_ExoCap_Jan31.2012; RL_EF_ExoCap_Jan31.2012 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#1.31.12_sample_for_HL114] * fq: genome-miner…')
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Data

  • Library: RL_Fib100c_29s_ExoCap_Jan31.2012; RL_EF_ExoCap_Jan31.2012 [1]
  • fq: genome-miner:/media/SeqStore2/120211_HL114/RL_Exome (s2 and s3)
  • Analysis: genome-miner:~/Ext12T/HL114

Mapping

  • Instruction: [2]
  • Script: fastq2fixedBam.pl (rmdup off; SNP call off)
  • Upload file: HL114.unix.info <for fastq2fixedBam.pl>; HL114_Athurva.unix.info <for latest version of variantCallerBwaGATK.pl>
tr "\r" "\n" < HL114.info > HL114.unix.info
tr "\r" "\n" < HL114_Athurva.info > HL114_Athurva.unix.info
  • Run:
nohup ./fastq2fixedBam.pl HL114.unix.info &> HL114.unix.status &
  • Output: HL114.fixed.bam
  • De-multiplexing: split_bam_file.pl
  • Output: HL114_index.fixed.bam

Genome coverage

  • Script: bam_to_pileup.pl
  • Input: HL114_index.fixed.bam
  • Output: HL114_index.pileup; HL114_(index).exom_cov_stat.txt

Amplification bias

  • Script: getBlockCoverage.pl
  • Input: HL114_index.pileup
  • Output: HL114_Indx.bedGraph.txt

SNP calling

  • Script: mPileup2sncTable.pl
  • Input: HL114_all index.pileup
  • Output: MM_libraries_snc_matrix_1.txt (>=1) MM_libraries_snc_matrix_2.txt (>=2)

Analysis

Basic stat

  • Take the two extremes as the example for analysis
HL114 Raw Reads Mapped Reads Mapping rate ' Genomic Coverage (1x) Genomic Coverage (8x) Genomic Coverage (20x) ' Exomic Coverage (1x) Exomic Coverage (8x) Exomic Coverage (20x) ExoCap (1x) ExoCap (8x) ExoCap (20x) %target_covered (1X) %target_covered (8X) %target_covered (20X)
Indx84 3,466,058 3,006,065 0.86728641 115,157,379 4,957,071 1,497,440 8,601,392 1,967,268 816,346 0.074692495 0.396860969 0.545161075 0.194945125 0.044586888 0.018501967
Indx80 1,164,032 954,899 0.820337413 51,214,017 1,279,455 309,971 5,429,531 625,099 168,536 0.106016503 0.488566616 0.54371538 0.123056896 0.014167475 0.003819762
Indx90 2,758,235 2,379,233 0.862592564 87,506,864 3,746,156 1,288,719 4,935,581 1,621,741 770,420 0.056402215 0.432908026 0.597818454 0.111861831 0.036755737 0.017461083
Indx92 454,131 384,678 0.847063953 10,043,141 741,152 249,113 722,367 211,249 119,838 0.071926402 0.285027903 0.481058797 0.016371992 0.004787825 0.002716053
Indx7 2,651,616 2,301,606 0.868001249 52,315,891 4,812,671 1,377,887 2,273,297 1,020,041 613,853 0.043453279 0.21194904 0.445503151 0.051522843 0.023118586 0.013912591
Indx8 621,535 281,492 0.452898067 7,429,177 606,175 187,171 547,137 115,081 52,532 0.073647054 0.189847816 0.280663137 0.012400515 0.002608238 0.001190605