User:Dpuiu: Difference between revisions

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= Test data sets =
= Test data sets =


Sanger (1)
'''Sanger (1)'''
* 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
* 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg  
* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg  


Sanger (2)
'''Sanger (2)'''
* 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
* 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg  
* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg  


Solexa unpaired
'''Solexa unpaired'''
* 2,659,250 36bp reads
* 2,659,250 36bp reads
* Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna
* Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna


* Solexa paired (1)
'''Solexa paired (1)'''
* 142,858 35bp reads;  
* 142,858 35bp reads;  
* assemble into one 99,995 ctg/scaff by velvet
* assemble into one 99,995 ctg/scaff by velvet
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa  
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa  


Solexa paired (2)
'''Solexa paired (2)'''
* 92,143 35bp reads;  
* 92,143 35bp reads;  
* assemble into 1 102,059 bp scaff by velvetp.sh  (velveth -shortPaired)
* assemble into 1 102,059 bp scaff by velvetp.sh  (velveth -shortPaired)
* assemble into 5 contigs by velvet.sh            (velveth)
* assemble into 5 contigs by velvet.sh            (velveth)
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa

Revision as of 16:29, 15 December 2009

Daniela Puiu's page

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Test data sets

Sanger (1)

  • 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
  • Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg

Sanger (2)

  • 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
  • Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg

Solexa unpaired

  • 2,659,250 36bp reads
  • Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna

Solexa paired (1)

  • 142,858 35bp reads;
  • assemble into one 99,995 ctg/scaff by velvet
  • Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa

Solexa paired (2)

  • 92,143 35bp reads;
  • assemble into 1 102,059 bp scaff by velvetp.sh (velveth -shortPaired)
  • assemble into 5 contigs by velvet.sh (velveth)
  • Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa