Difference between revisions of "SAM or BAM alignment file"

From BioUML platform
Jump to: navigation, search
(Plugin link added)
(Automatic synchronization with BioUML)
 
(2 intermediate revisions by one user not shown)
Line 1: Line 1:
 
;File format title
 
;File format title
 
:SAM or BAM alignment file (*.sam, *.bam)
 
:SAM or BAM alignment file (*.sam, *.bam)
 +
;Element type
 +
:{{Type link|track}}
 
;Plugin
 
;Plugin
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
Line 13: Line 15:
 
* '''Properties''' – Additional importer parameters
 
* '''Properties''' – Additional importer parameters
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
** '''Sequence collection''' – Sequence collection
+
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 
** '''Genome ID string''' – Something like <nowiki>'</nowiki>hg18<nowiki>'</nowiki> or <nowiki>'</nowiki>mm6<nowiki>'</nowiki>
 
** '''Genome ID string''' – Something like <nowiki>'</nowiki>hg18<nowiki>'</nowiki> or <nowiki>'</nowiki>mm6<nowiki>'</nowiki>
 
** '''Create index''' – Create index (can take a long time)
 
** '''Create index''' – Create index (can take a long time)

Latest revision as of 17:17, 6 June 2013

File format title
SAM or BAM alignment file (*.sam, *.bam)
Element type
Type-track-icon.png track
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] SAM or BAM alignment file (*.sam, *.bam)

Import SAM/BAM file

[edit] Parameters:

  • File to import – Specify file from your computer
  • Target – Path in repository to put imported file to
  • Properties – Additional importer parameters
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
    • Genome ID string – Something like 'hg18' or 'mm6'
    • Create index – Create index (can take a long time)
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox