User:Dpuiu: Difference between revisions

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Daniela Puiu's page
Daniela Puiu's page


= Bookmarks =
 
[[NCBI_submission|NCBIsub]] ;
[[Culex_pipiens_symbiont|wPip]] ;
[[Dpuiu_definitions|Definitions]] ;
[[Pop_group_meeting|Pop]] ;
[[dpuiu_Perl|Perl]] ;
[[dpuiu_C|C]] ;
[[dpuiu_Linux|Linux]];
[[dpuiu_R|R]];
[http://www.bioperl.org/wiki/HOWTOs BioPerl HOWTOs];
[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB computers]


= NCBI =
= NCBI =
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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 ...


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* [[Yersinia_pestis|Yersinia pestis]]
* [[Yersinia_pestis|Yersinia pestis]]


<!--
'''Other genomes'''
'''Other genomes'''
* [[Bumblebee|Bombus impatiens]]
* [[Bumblebee|Bombus impatiens]]
* [[Brugia_malayi|Brugia malayi]]
* [[Brugia_malayi|Brugia malayi]]
* [[Bos_taurus|Bos taurus]] , [[Bos_taurus_redo|Bos taurus redo]] , [[Bos_taurus_3.0|Bos taurus 3.0]]
* [[Bos_taurus|Bos taurus]] , [[Bos_taurus_redo|Bos taurus redo]] , [[Bos_taurus_3.0|Bos taurus 3.0]]
* [[dpuiu_cat|Cat]]
* [[Coffee_bacs|Coffee BACs]]
* [[Coffee_bacs|Coffee BACs]]
* [[Culex_pipiens_symbiont|Culex pipiens wolbachia symbiont]]
* [[Culex_pipiens_symbiont|Culex pipiens wolbachia symbiont]]
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* [[Megachile_rotundata|Megachile rotundata]]
* [[Megachile_rotundata|Megachile rotundata]]
* [[Methanobrevibacter_smithii|Methanobrevibacter smithii]]
* [[Methanobrevibacter_smithii|Methanobrevibacter smithii]]
* [[Pine_tree|Pine tree]]
* [[Pseudomonas_aeruginosa|Pseudomonas aeruginosa]]
* [[Pseudomonas_aeruginosa|Pseudomonas aeruginosa]]
* [[Pseudodomonas_syringae|Pseudomonas syringae]]
* [[Pseudodomonas_syringae|Pseudomonas syringae]]
* [[Sea_urchin|Sea urchin]]
* [[Sea_urchin|Sea urchin]]
* [[Turkey|Turkey]]
* [[Turkey|Turkey]]
* [[Xanthomonas_oryzae|Xanthomonas oryzae]]
* [[Xanthomonas_oryzae|Xanthomonas oryzae]] XOO
* [[Xanthomonas_campestris_pv_raphani|Xanthomonas campestris pv. raphani]] XCR
* [[Strawberry|Strawberry]]
* [[Strawberry|Strawberry]]
* [[Ecoli_germany|Ecoli Germany]]
-->


= Other =
= Other =
* [[Trace_formatting|Sequencing]]  
* [[Trace_formatting|Sequencing]]  
* [[dpuiu_alignment|Alignment]] *
* [[dpuiu_CA|CA]] ; [[Assembly_merge|Assembly]]
* [[dpuiu_CA|CA]] ; [[Assembly_merge|Assembly]]
* [[dpuiu_Assemblathon|Assemblathon]]
* [[dpuiu_HTS|HTS]]
* [[Comparative_assemblies|Comparative assemblies]]
* [[Comparative_assemblies|Comparative assemblies]]
* [[Metagenoms|Metagenomics]]
* [[Metagenoms|Metagenomics]]
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* [[Vector_trimming|Vector trimming]]
* [[Vector_trimming|Vector trimming]]
* [[Data_formats|Data formats]]
* [[Data_formats|Data formats]]
 
<!--
* [[dpuiu_Assemblathon|Assemblathon]]
* [[dpuiu_HTS|HTS]]
* [[dpuiu_definitions|Definitions]]
* [[dpuiu_definitions|Definitions]]
* [[dpuiu_meeting_notes|Meeting notes]]
* [[dpuiu_meeting_notes|Meeting notes]]
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* [[dpuiu_CS|CS]] ; [[dpuiu_Perl|Perl]] ; [[dpuiu_C|C]] ; [[dpuiu_Linux|Linux]] ; [[dpuiu_DOS|DOS]] ; [[douiu_wiki|wiki]] ; [[dpuiu_thunderbird|thunderbird]]
* [[dpuiu_CS|CS]] ; [[dpuiu_Perl|Perl]] ; [[dpuiu_C|C]] ; [[dpuiu_Linux|Linux]] ; [[dpuiu_DOS|DOS]] ; [[douiu_wiki|wiki]] ; [[dpuiu_thunderbird|thunderbird]]
* [[Pop_group_meeting|Pop group meeting]] (Monday 's 3pm)
* [[Pop_group_meeting|Pop group meeting]] (Monday 's 3pm)
 
* [[dpuiu_snp|Snp calling]]
* [[dpuiu_todo|ToDo]]
* [[dpuiu_todo|ToDo]]
 
* [[dpuiu_JHU|JHU]]
= 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'''
* [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001087 E coli Whole Genome Sequencing on 454 and Illumina]
* Location /fs/szattic-asmg4/dpuiu/Ecoli

Latest revision as of 15:34, 27 December 2011

Daniela Puiu's page


NCBI

Links

  • ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes


Other

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