Changes between Version 35 and Version 36 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 13:32:08 (7 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -41 +41 @@
 {{{
 
-bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir2ndPass --genomeFastaFiles /path/to/genome/fasta1 --sjdbFileChrStartEnd /path/to/first/pass/directory/SJ.out.tab --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDirSecondPass --genomeFastaFiles /path/to/genome/fasta1 --sjdbFileChrStartEnd /path/to/first/pass/directory/SJ.out.tab --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
 }}}
 
@@ -48 +48 @@
 {{{
 Input format: fastq ; output format: SAM
-bsub STAR --genomeDir /path/to/GenomeDir2ndPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDirSecondPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}