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

From ZhangLabWiki
Jump to navigation Jump to search
>Noi
No edit summary
>Noi
Line 10: Line 10:
  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. Then I tried again by putting the concatenated file on /media/Ext12T/Noi_scratch2/Noi_ASM_Mysql-database which has a lot of space available.
*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.
12878.libraryinfo.txt content
/media/Ext12T/Noi_scratch2/Noi_ASM_Mysql-database/12878.fastq 1

Revision as of 05:35, 2 March 2012

ASM analysis of WGBB12878

  • 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;
  • 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.