Changes between Version 48 and Version 49 of SOPs/mapping

Timestamp:

06/07/17 12:08:53 (8 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -225 +225 @@
   * '''--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.  
   * '''--runThreadN <n> ''' Specifies the number of threads to use.
+  * '''--readFilesCommand <cmd> ''' Specifies the command to uncompress compressed fastq files.
+  * '''--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)
+