Changes between Version 62 and Version 63 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/06/17 09:02:09 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v62 v63  
    99== Using GATK to call variants from RNA-seq reads ==
    1010This example pipeline starts with a single-end short-read fastq file (Reads_1.fq).
    11 \\ \\
    12 Note that '''GATK requires Java 1.8'' (so you may need to adjust your path to point to that version, if an older version is the default).\\
     11\\
     12Note that GATK requires Java 1.8 (so you may need to adjust your path to point to that version, if an older version is the default).\\
    1313For example, this can be added to ~/.bashrc: \\
    1414export PATH=/path/to/java:$PATH
    15 \\ \\
    16 
     15\\
    1716
    1817'''1 - Run the STAR 2-pass procedure to map reads to the reference genome.'''