Noi/NOTES/2012-2-29: Difference between revisions

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'''Link to calendar:'''[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]]
= ASM analysis of WGBB12878 =
= ASM analysis of WGBB12878 =
* Directory: '''/media/SeqStore2/120209_HiSeq/HL_WGBS/'''
* Directory: '''/media/SeqStore2/120209_HiSeq/HL_WGBS/'''
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  my $root = "/home/expresso/Noi_ASM/WGBS_12878/";
  my $root = "/home/expresso/Noi_ASM/WGBS_12878/";
  my $readlength = 100;
  my $readlength = 100;
*Note: After finishing concatenate sequencing data into 12878.fastq, I got only 23.9 Gb data. I repeated again, but got the same amount of data, I guess that it possible that the space on expresso is not enough to put the whole data.
*Note: After finishing concatenate sequencing data into 12878.fastq, I got only 23.9 Gb data. I repeated again, but got the same amount of data. The problem was resolved by splitting the read into different chromosomes based on the size of each one as described by Dinh's page: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-5

Latest revision as of 16:34, 19 June 2012

Link to calendar:[[1]]

ASM analysis of WGBB12878[edit]

  • Directory: /media/SeqStore2/120209_HiSeq/HL_WGBS/
s_7_1_sequence.txt.gz
s_7_2_sequence.txt.gz
s_8_1_sequence.txt.gz
s_8_2_sequence.txt.gz
  • Concatenate and uncompressed data (no trimming required)
nohup less /media/SeqStore2/120209_HiSeq/HL_WGBS/*.gz > 12878.fastq
  • In Master Execution Script, PipelineExecute-NP.pl
my $root = "/home/expresso/Noi_ASM/WGBS_12878/";
my $readlength = 100;