Sha256: e1a8671924b051b8edf266962042500dc37c3bb40f164e889457e0ba48a043ca
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Size: 1.63 KB
Versions: 11
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Stored size: 1.63 KB
Contents
# ====================================== # General parameters TRANSCRIPTOMICS # ====================================== # Help: <br/>This template is used to preprocess Roche 454 transcriptomic data <br/> # Help: <br/><b>Plugin list and aplication order:</b><br/> # Help: <ul> # Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li> # Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li> # Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li> # Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li> # Help: <li>PluginAdapters: trimming the adapters found in SeqTrimNEXT database</li> # Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li> # Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li> # Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li> # Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li> # Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li> # Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li> # Help: </ul> plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity contaminants_db="contaminants.fasta cont_ribosome.fasta"
Version data entries
11 entries across 11 versions & 1 rubygems