Difference between revisions of "User:Dpuiu"

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* [[Vector_trimming|Vector trimming]]
 
* [[Vector_trimming|Vector trimming]]
 
* [[Data_formats|Data formats]]
 
* [[Data_formats|Data formats]]
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* [[dpuiu_definitions|Definitions]]
 
* [[dpuiu_definitions|Definitions]]
 
* [[dpuiu_meeting_notes|Meeting notes]]
 
* [[dpuiu_meeting_notes|Meeting notes]]
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* [[dpuiu_snp|Snp calling]]
 
* [[dpuiu_snp|Snp calling]]
 
* [[dpuiu_todo|ToDo]]
 
* [[dpuiu_todo|ToDo]]
 
 
* [[dpuiu_JHU|JHU]]
 
* [[dpuiu_JHU|JHU]]
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= CBCB software =
 
= CBCB software =

Revision as of 15:32, 27 December 2011

Daniela Puiu's page


NCBI

Links

  • ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes


Other

CBCB software

  • Link
 https://wiki.umiacs.umd.edu/cbcb/index.php/Communal_Software#Core_Software
  • Locations
 /fs/szdevel/core-cbcb-software
 /fs/sz-user-supported
  • Change group
   $ groups
     dpuiu cbcb-staff cbcb cbcbwww

   $ newgroup cbcb-staff
      # creates a  new shell; 
   $ ^D
  • After install ...
 find /fs/szdevel/core-cbcb-software | xargs chgrp cbcb-staff
 find /fs/szdevel/core-cbcb-software | xargs chmod o-w

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 scaff by velvetp.sh (velveth -shortPaired)
  • assemble into 5 contigs by velvet.sh (velveth)
  • Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa

Solexa & 454