Changes between Version 57 and Version 58 of SOPs/mapping


Ignore:
Timestamp:
01/09/18 14:48:10 (7 years ago)
Author:
byuan
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/mapping

    v57 v58  
    174174  * '''--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. 
    175175  * '''--runThreadN <n> ''' Specifies the number of threads to use.
    176   * '''--readFilesCommand <cmd> ''' Specifies the command to uncompress compressed fastq files.
     176  * '''--readFilesCommand <cmd> ''' Specifies the command to uncompress compressed fastq files. For gzipped files (*.gz) use --readFilesCommand gunzip -c.
    177177  * '''--outSAMtype <BAM sortingMode> ''' Specifies the type of BAM file to create.  Options: 'BAM Unsorted', 'BAM SortedByCoordinate', 'BAM Unsorted SortedByCoordinate' (to create both unsorted and sorted BAMs)
    178178