Changes between Version 21 and Version 22 of SOPs/SAMBAMqc


Ignore:
Timestamp:
04/27/17 09:47:33 (8 years ago)
Author:
thiruvil
Comment:

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  • SOPs/SAMBAMqc

    v21 v22  
    6262   java -jar picard.jar CollectRnaSeqMetrics INPUT=bamFile REF_FLAT=refFlatFile STRAND_SPECIFICITY=NONE OUTPUT=outputFile REFERENCE_SEQUENCE=/path/to/genome.fa CHART_OUTPUT=output.pdf VALIDATION_STRINGENCY=SILENT
    6363   # Example command
    64    java -jar /usr/local/share/picard-tools/picard.jar CollectRnaSeqMetrics INPUT=WT.bam REF_FLAT=/nfs/genomes/mouse_mm10_dec_11_no_random/anno/refFlat.txt STRAND_SPECIFICITY=NONE OUTPUT=QC_metrics/WT.RnaSeqMetrics.txt REFERENCE_SEQUENCE=/nfs/genomes/mouse_mm10_dec_11_no_random/fasta_whole_genome/mm10.fa CHART_OUTPUT=QC_metrics/WT.RnaSeqMetrics.pdf VALIDATION_STRINGENCY=SILENT
     64   java -jar /usr/local/share/picard-tools/picard.jar CollectRnaSeqMetrics INPUT=WT.bam REF_FLAT=/nfs/genomes/mouse_mm10_dec_11_no_random/anno/refFlat.txt STRAND_SPECIFICITY=NONE OUTPUT=QC_metrics/WT.RnaSeqMetrics.txt CHART_OUTPUT=QC_metrics/WT.RnaSeqMetrics.pdf VALIDATION_STRINGENCY=SILENT
    6565
    6666}}}