Changes between Version 5 and Version 6 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 09:55:32 (8 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -12 +12 @@
 export PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:$PATH
 \\ \\
+
+1 - '''Index the reference genome for '''First Pass'''.'''
+
+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 --sjdbOverhang 100 --runThreadN 8 
+}}}
+
+The parameters included in the above sample command are:
+  * '''--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.