Difference between revisions of "User:Dpuiu"

From Cbcb
Jump to navigation Jump to search
Line 86: Line 86:
 
-->
 
-->
  
= 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 =
 
= Test data sets =

Revision as of 15:32, 27 December 2011

Daniela Puiu's page


NCBI

Links

  • ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes


Other


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