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  • ...ncludes a starting VMware image, and uses the example data that comes with SAMtools.
    10 KB (1,396 words) - 17:18, 2 December 2013
  • sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2 libapache2-mod-fcgid libxml-sax-writer-perl libxml-xpathengine-perl libyaml-syck-perl samtools
    8 KB (799 words) - 20:37, 8 August 2018
  • ...e Alignment/Map (SAM)]]'' format. BAM and SAM are both part of [[#SAMtools|SAMtools]]. BAM is compressed, binary, indexed format for [[Next Generation Sequenc ...rmat for [[Next Generation Sequencing]] data. It is a part of [[#SAMtools|SAMtools]]. [[GBrowse]] 2 has an adaptor that can read SAM data.
    14 KB (2,081 words) - 02:50, 14 March 2014
  • | [http://samtools.sourceforge.net/ SAMtools]
    3 KB (443 words) - 16:22, 7 August 2012
  • ...on next generation sequencing, including [http://samtools.sourceforge.net SAMtools], BWA, and [http://maq.sourceforge.net MAQ].</div> ...: Sequence alignment/map format (SAM) and [http://samtools.sourceforge.net SAMtools]
    59 KB (8,741 words) - 19:37, 4 September 2013
  • ...des a starting [[VMware]] image, and uses the example data that comes with SAMtools.
    2 KB (236 words) - 17:10, 18 December 2013
  • ...on [[August 2009 GMOD Meeting#Visualising NGS Data in GBrowse 2|using SAM/SAMtools in GBrowse]].
    2 KB (301 words) - 19:37, 4 September 2013
  • ...tion Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
    4 KB (542 words) - 23:11, 9 October 2012
  • ...ep instructions for visualizing the example human data that comes with the SAMtools package.
    1 KB (156 words) - 23:10, 9 October 2012
  • ...ncludes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by [[Galaxy]] team.
    2 KB (239 words) - 23:09, 9 October 2012
  • ...rowse]] 2 to visualize NGS data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This includes a [[VMware]] image to work w ...) and SAMtools|Quest for Standard: Sequence alignment/map format (SAM) and SAMtools]]
    3 KB (450 words) - 00:52, 18 November 2010
  • * samtools, and its dependency libncurses5-dev $ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download
    9 KB (1,327 words) - 22:46, 3 October 2012
  • ...eration Sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. ...urceforge.net SAMtools]. We'll use the example human data that comes with SAMtools to do that. First we'll load the reference sequence and some gene models.
    38 KB (5,742 words) - 18:11, 9 October 2012
  • *[http://samtools.sourceforge.net/ BAM or SAM] (for sequence alignment data) ...ompact, fast to read way, as part of the [http://samtools.sourceforge.net/ SAMtools] project.
    17 KB (2,763 words) - 18:52, 8 October 2012
  • ** SQLite, SAMtools (NGS) adaptors
    100 KB (14,725 words) - 17:31, 30 November 2012
  • ...equires the C Samtools library. See http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.35/README for details.
    23 KB (3,672 words) - 14:44, 10 July 2013
  • Install Samtools ....16.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.16/samtools-0.1.16.tar.bz2/download
    15 KB (2,338 words) - 18:52, 8 October 2012
  • * [[GBrowse]] 2.54 (with samtools, BigWig and fastCGI support)
    982 B (152 words) - 19:14, 14 June 2013
  • Syntax used to import a indexed fasta(i.e. a fasta file where you run `samtools faidx yourfile.fa` which outputs yourfile.fa.fai) .... Exactly one of these three options must be used. With indexed_fasta, the samtools faidx yourfile.fa must be run before hand. With twobit, the twobit file wil
    185 KB (26,471 words) - 15:29, 6 July 2018
  • ...xy]] to run Bowtie and produce a SAM file. In order to use this tutorial, SAMtools and Bio::DB::Sam must be installed. This is based on the [[GBrowse_NGS_Tut samtools faidx volvox.fa
    5 KB (853 words) - 00:19, 23 October 2012
  • * samtools, and its dependency libncurses5-dev
    14 KB (1,948 words) - 20:48, 27 August 2013
  • ...ncludes a starting VMware image, and uses the example data that comes with SAMtools.
    8 KB (1,065 words) - 18:35, 10 September 2013
  • ===Updating SAMtools=== The version of SAMtools may need to be updated. Get the samtools release:
    7 KB (932 words) - 22:50, 13 February 2013
  • * samtools, and its dependency libncurses5-dev $ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2
    9 KB (1,328 words) - 17:58, 14 February 2013
  • ...ve run prepare-refseqs.pl on a FASTA file. Instead you can simply use the "samtools faidx" program to index your fasta file in a data directory, and set trackL To create an Indexed FASTA, install samtools and run
    66 KB (10,453 words) - 15:51, 21 July 2018
  • * samtools, and its dependency libncurses5-dev
    14 KB (1,931 words) - 00:01, 20 February 2014
  • * samtools, and its dependency libncurses5-dev
    13 KB (1,905 words) - 14:21, 21 May 2014
  • ...to use Indexed FASTA (selecting both a fasta and a fai file generated by `samtools faidx file.fasta`) or 2bit. Even small genomes with normal FASTA will be mu
    3 KB (528 words) - 22:30, 19 July 2018

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