Changes between Version 20 and Version 21 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 12:36:11 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v20 v21  
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    3935The parameters included in the above sample commands are:
    4036  * '''--runMode <alignReads, genomeGenerate>'''   "alignReads" does the actual mapping. "genomeGenerate" generates the genomeDir required for mapping (default = alignReads).
    … …  
    4238  * '''--genomeFastaFiles <genome FASTA files>''' Specifies genome FASTA files to be used.
    4339  * '''--readFilesIn <read1.fastq read2.fastq> ''' Specifies the fastq files containing the reads, can be single-end or paired-end.
    44   * '''--sjdbScore <n> ''' Provides extra alignment score for alignments that cross database junctions (default = 2). If this score is positive, it will bias the alignment toward annotated junctions. This is only used if during the genomeGenerate step a splice junction annotation file is used. 
    4540  * '''--runThreadN <n> ''' Specifies the number of threads to use.