Changes between Version 29 and Version 30 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 13:07:04 (8 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v29 v30  
    2828}}}
    2929
    30 The parameters included in the above sample command are:
    31   * '''--sjdbOverhang  ''' Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database.  For short reads (<50) use readLength - 1, otherwise a generic value of 100 will work as well (see manual for more info).
    32   * '''--sjdbGTFfile <GTF_file.gtf>''' Supplies STAR with a GTF file during the genomeGenerate step.  Combined with the --sjdbScore <n> option during mapping, this will bias the alignment toward annotated junctions, and reduces alignment to pseudogenes.
    3330
    3431To map:
    … …  
    4946
    5047The parameters included in the above sample commands are:
     48  * '''--sjdbOverhang  ''' Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database.  For short reads (<50) use readLength - 1, otherwise a generic value of 100 will work as well (see manual for more info).
     49  * '''--sjdbGTFfile <GTF_file.gtf>''' Supplies STAR with a GTF file during the genomeGenerate step.  Combined with the --sjdbScore <n> option during mapping, this will bias the alignment toward annotated junctions, and reduces alignment to pseudogenes.
    5150  * '''--runMode <alignReads, genomeGenerate>'''   "alignReads" does the actual mapping. "genomeGenerate" generates the genomeDir required for mapping (default = alignReads).
    5251  * '''--genomeDir </path/to/GenomeDir>'''  Specifies the path to the directory used for storing the genome information created in the genomeGenerate step.