Changes between Version 29 and Version 30 of SOPs/mapping

Timestamp:

07/12/16 15:14:18 (9 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -171 +171 @@
 To generate genome index files for STAR:
 {{{
-bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --sjdbGTFfile /path/to/GTF/FileName.gtf --runThreadN 8
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 39 --runThreadN 8 
 }}}
 To map:
@@ -186 +186 @@
   * '''--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.
+  * '''--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).