Changes between Version 55 and Version 56 of SOPs/mapping

Timestamp:

09/29/17 12:34:22 (7 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -206 +206 @@
 {{{
 bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
+
+#generate index without overhang/gtf, specify these at mapping instead
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --runThreadN 8 
+
 }}}
 
@@ -218 +222 @@
 # 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 gunzip -c --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 gunzip -c --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang readLength-1
+
 }}}