Difference between revisions of "CH391L/UTpond"

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(Analysis tool)
 
(4 intermediate revisions by one user not shown)
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* V3BC24:  562,803 (F3), 525,892 (F5),  588,304 (raw)
 
* V3BC24:  562,803 (F3), 525,892 (F5),  588,304 (raw)
 
* V3BC25:  569,125 (F3), 531,015 (F5),  595,064 (raw)
 
* V3BC25:  569,125 (F3), 531,015 (F5),  595,064 (raw)
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You can download CSFASTA files from [http://www.marcottelab.org/users/CH391L/UTpond/raw/ here].
  
 
== Databases ==
 
== Databases ==
* Prokaryotes:  
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* Prokaryotes: http://www.marcottelab.org/users/CH391L/UTpond/NCBI.bacteria/NCBI_bacteria_rep.tgz <b>(835 MB)</b> (870 genomes)
* Eukaryotes:
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** Source: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (2011-Feb-28 version).
* Viruses:  
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** Select one chromosome per species randomly.
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* Eukaryotes (Organelle): http://www.marcottelab.org/users/CH391L/UTpond/ENA.organelle/ENA_organelle.fna.gz (2,982 genomes)
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** Source: http://www.ebi.ac.uk/genomes/organelle.html
  
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== Mapping results (SAM file + read_freq) ==
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* Prokaryotes: http://www.marcottelab.org/users/CH391L/UTpond/NCBI.bacteria/
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* Eukaryotes: http://www.marcottelab.org/users/CH391L/UTpond/ENA.organelle/
  
 
== Analysis tool ==
 
== Analysis tool ==
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** [http://samtools.sourceforge.net/SAM-1.3.pdf Specification PDF]
 
** [http://samtools.sourceforge.net/SAM-1.3.pdf Specification PDF]
 
** [http://bioinformatics.oxfordjournals.org/content/25/16/2078.long Paper]
 
** [http://bioinformatics.oxfordjournals.org/content/25/16/2078.long Paper]
* SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/ <b><font color='red'>Never, ever run this program on cygnus. It needs lots of memory, so easily kills the computer.</font></b>
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* SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/  
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** <b><font color='red'>Never, ever try to run this program on cygnus. It needs lots of memory, so easily kills the computer.</font></b>
 
** [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000386 Paper for original version]
 
** [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000386 Paper for original version]
 
** [http://bioinformatics.oxfordjournals.org/content/early/2011/01/28/bioinformatics.btr046 Paper for version 2]
 
** [http://bioinformatics.oxfordjournals.org/content/early/2011/01/28/bioinformatics.btr046 Paper for version 2]

Latest revision as of 16:43, 28 March 2011

Contents

Number of reads

  • V3BC21: 213,419 (F3), 199,158 (F5), 223,100 (raw)
  • V3BC22: 634,431 (F3), 595,251 (F5), 661,120 (raw)
  • V3BC23: 1,015,471 (F3), 951,357 (F5), 1,060,308 (raw)
  • V3BC24: 562,803 (F3), 525,892 (F5), 588,304 (raw)
  • V3BC25: 569,125 (F3), 531,015 (F5), 595,064 (raw)

You can download CSFASTA files from here.

Databases

Mapping results (SAM file + read_freq)

Analysis tool

$ gsmapper-cs foobar.csfasta db.fasta -E -N 4 -o 1000 -h 80% >foobar.gsmapper_sam 2>foobar.gsmapper_log