Changes between Version 19 and Version 20 of SOP/CallingVariantsRNAseq

Timestamp:

08/16/17 12:35:06 (8 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -19 +19 @@
 {{{
 
-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 
+bsub STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 --sjdbGTFfile /path/to/GTF/FileName.gtf --sjdbOverhang 100 --runThreadN 8 
 }}}
 
@@ -32 +32 @@
 bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}
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+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).
+  * '''--genomeDir </path/to/GenomeDir>'''  Specifies the path to the directory used for storing the genome information created in the genomeGenerate step.
+  * '''--genomeFastaFiles <genome FASTA files>''' Specifies genome FASTA files to be used.
+  * '''--readFilesIn <read1.fastq read2.fastq> ''' Specifies the fastq files containing the reads, can be single-end or paired-end.
+  * '''--sjdbScore <n> ''' Provides extra alignment score for alignments that cross database junctions (default = 2). If this score is positive, it will bias the alignment toward annotated junctions. This is only used if during the genomeGenerate step a splice junction annotation file is used.  
+  * '''--runThreadN <n> ''' Specifies the number of threads to use.