Changes between Version 63 and Version 64 of SOPs/mapping

Timestamp:

06/12/19 14:16:55 (6 years ago)

Author:

byuan

Comment:

--

SOPs/mapping

@@ -111 +111 @@
   * '''--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).
   * '''--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.
+  * '''--alignIntronMax''' maximum intron length needs to be adjusted in certain species, such as yeast.
+  * '''--genomeSAindexNbases''' For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical value of min(14, log2(GenomeLength)/2 - 1).
 
 To map: