Changes between Version 58 and Version 59 of SOP/CallingVariantsRNAseq

Timestamp:

09/06/17 07:49:12 (7 years ago)

Author:

krichard

Comment:

--

SOP/CallingVariantsRNAseq

@@ -32 +32 @@
     '''Run this command within the FirstPass directory'''
 {{{
-bsub STAR --genomeDir /path/to/GenomeDirFirstPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDirFirstPass --readFilesIn /path/to/Reads_1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}
 
@@ -48 +48 @@
 {{{
 Input format: fastq ; output format: SAM
-bsub STAR --genomeDir /path/to/GenomeDirSecondPass --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
+bsub STAR --genomeDir /path/to/GenomeDirSecondPass --readFilesIn /path/to/Reads_1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8
 }}}
 
@@ -59 +59 @@
   * '''--genomeFastaFiles <genome FASTA files>''' Specifies genome FASTA files to be used.
   * '''--sjdbFileChrStartEnd <output from first pass>  '''  path to the file with genomic coordinates for introns
-  * '''--readFilesIn <read1.fastq read2.fastq> ''' Specifies the fastq files containing the reads, can be single-end or paired-end.
+  * '''--readFilesIn <Reads_1.fastq read2.fastq> ''' Specifies the fastq files containing the reads, can be single-end or paired-end.
   * '''--runThreadN <n> ''' Specifies the number of threads to use.