Changes between Version 60 and Version 61 of SOPs/mapping

Timestamp:

01/22/19 10:47:50 (6 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -115 +115 @@
 {{{
 # Input format: fastq ; output format: SAM
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq /path/to/read2.fastq --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq /path/to/read2.fastq --outFileNamePrefix whateverPrefix --sjdbScore 2 --runThreadN 8
 # Input format: fastq.gz ; output format: BAM (sorted by position)
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --outFileNamePrefix whateverPrefix --sjdbScore 2 --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
 
 #mapping when gtf/overhang was not specified during indexing
-bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --sjdbScore 2 --outFileNamePrefix whateverPrefix --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang readLength-1
+bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fq.gz /path/to/read2.fq.gz --outFileNamePrefix whateverPrefix --sjdbScore 2 --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang readLength-1
 
 }}}
@@ -149 +149 @@
     '''Run this command within the FirstPass directory'''
 {{{
-bsub STAR --genomeDir /path/to/GenomeDirFirstPass --readFilesIn /path/to/Reads_1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDirFirstPass --readFilesIn /path/to/Reads_1.fastq --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}