SAMSWiki/WebDocumentation/IntroDuction/PreProcessing: Difference between revisions
Jump to navigation
Jump to search
imported>VirginieMittard No edit summary |
m (3 revisions) |
||
| (2 intermediate revisions by one other user not shown) | |||
| Line 11: | Line 11: | ||
** mitochondrial DNA | ** mitochondrial DNA | ||
** ribosomal DNA | ** ribosomal DNA | ||
Here are the subsections: | |||
* /QualityClipping | |||
** [[/PHRED]] | |||
** /Trace2Dbest | |||
* /VectorClipping | |||
** /VecScreen | |||
** [[/XBLAST]] | |||
* /RepeatMasker | |||
* [[/Vector and Repeat masking]] | |||
** /CrossMatch | |||
** [[/Vmatch]] | |||
Latest revision as of 07:17, 26 October 2011
The pre-processing part consists in several steps such as:
- cutting low quality parts (usually beginning and end)
- cutting or masking vector and adaptor sequences
- masking repeats
- masking low complexixity regions such as poly A tails
- masking contaminating sequences:
- bacterial DNA
- yeast DNA
- mitochondrial DNA
- ribosomal DNA
Here are the subsections:
- /QualityClipping
- /PHRED
- /Trace2Dbest
- /VectorClipping
- /VecScreen
- /XBLAST
- /RepeatMasker
- /Vector and Repeat masking
- /CrossMatch
- /Vmatch