Changes between Version 25 and Version 26 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 13:01:20 (8 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -19 +19 @@
 {{{
 
-bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDirFirstPass --genomeFastaFiles /path/to/genome/fasta1 --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
 }}}
 
@@ -29 +29 @@
     '''Run this command within the FirstPass directory'''
 {{{
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDirFirstPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}
 
@@ -38 +38 @@
 {{{
 
-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 
+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 
 }}}
 
@@ -55 +55 @@
 {{{
 Input format: fastq ; output format: SAM
-bsub STAR --genomeDir /path/to/GenomeDir2nd --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDir2ndPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}