Changes between Version 9 and Version 10 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 12:28:53 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v9 v10  
    1818To generate genome index files for STAR:
    1919{{{
    20        '' Run this command within the "FirstPass" directory:'' ''''''
     20
    2121bsub 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
    2222}}}
    … …  
    2828To map:
    2929{{{
    30 # Input format: fastq ; output format: SAM
     30'''''Run this command within the "FirstPass" directory''
     31'''# Input format: fastq ; output format: SAM
    3132bsub STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/to/read1.fastq  --outFileNamePrefix whateverPrefix --runThreadN 8