Changes between Version 12 and Version 13 of SOPs/SAMBAMqc

Timestamp:

08/11/16 11:58:01 (9 years ago)

Author:

gbell

Comment:

--

SOPs/SAMBAMqc

@@ -45 +45 @@
    # output: CollectInsertSizeMetrics.txt: values for -r and --mate-std-dev can be found in this text file
    #         CollectInsertSizeMetrics_hist.pdf: insert size histogram (graphic representation)
-bsub java -jar  /usr/local/share/picard-tools/CollectInsertSizeMetrics.jar I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf
+bsub java -jar /usr/local/share/picard-tools/picard.jar CollectInsertSizeMetrics I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf
 }}}
 
@@ -59 +59 @@
 {{{
    # Usage:
-   java -jar /usr/local/share/picard-tools/CollectRnaSeqMetrics.jar INPUT=bamFile REF_FLAT=refFlatFile STRAND_SPECIFICITY=NONE OUTPUT=outputFile REFERENCE_SEQUENCE=/path/to/genome.fa CHART_OUTPUT=output.pdf VALIDATION_STRINGENCY=SILENT
+   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
    # Example command
-   java -jar /usr/local/share/picard-tools/CollectRnaSeqMetrics.jar 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
+   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
 
 }}}