Changes between Version 7 and Version 8 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 12:26:49 (7 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -14 +14 @@
 
 1 - '''Index the reference genome for First Pass.'''
+        Create folder, "FirstPass" before running these commands. 
 
 To generate genome index files for STAR:
@@ -23 +24 @@
   * '''--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.
+
+To map:
+{{{
+# Input format: fastq ; output format: SAM
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8