Changes between Version 21 and Version 22 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 12:45:20 (7 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -33 +33 @@
 }}}
 
+2 - '''Index the reference genome for Second Pass.'''
+        Create folder, "SecondPass" before running these commands. 
+
+To generate the 2nd pass genome index files for STAR:
+{{{
+
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir2nd --genomeFastaFiles /path/to/genome/fasta1 --sjdbFileChrStartEnd /path/to/first/pass/directory/SJ.out.tab --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
+}}}
+
+
 The parameters included in the above sample commands are:
   * '''--runMode <alignReads, genomeGenerate>'''   "alignReads" does the actual mapping. "genomeGenerate" generates the genomeDir required for mapping (default = alignReads).
@@ -39 +49 @@
   * '''--readFilesIn <read1.fastq read2.fastq> ''' Specifies the fastq files containing the reads, can be single-end or paired-end.
   * '''--runThreadN <n> ''' Specifies the number of threads to use.
+
+
+