Difference between revisions of "User:Dpuiu"

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* [http://www.sanger.ac.uk/ Sanger]
 
* [http://www.sanger.ac.uk/ Sanger]
 
* [http://www.sanger.ac.uk/Projects/Microbes/ Sanger Microbial Genomes]
 
* [http://www.sanger.ac.uk/Projects/Microbes/ Sanger Microbial Genomes]
* [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB]
+
 
** NCBI complete genomes: /fs/szdata//ncbi/genomes/Bacteria/  (*.fna)
 
** www -> /fs/www-cbcb/htdocs/
 
** Personal web site http://www.cbcb.umd.edu/~dpuiu -> /fs/www/users/dpuiu/
 
** Personal ftp site ftp://ftp.cbcb.umd.edu/pub/data/dpuiu -> /fs/ftp-cbcb/pub/data/dpuiu/
 
 
 
* [http://www.thearkdb.org/arkdb/index.jsp ARKDB] genetic maps - cow, chicken ...
 
* [http://www.thearkdb.org/arkdb/index.jsp ARKDB] genetic maps - cow, chicken ...
  

Revision as of 15:30, 27 December 2011

Daniela Puiu's page


NCBI

Links

  • ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes

Other 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