Changes between Version 31 and Version 32 of SOPs/miningSAMBAM


Ignore:
Timestamp:
02/11/16 14:21:30 (9 years ago)
Author:
gbell
Comment:

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  • SOPs/miningSAMBAM

    v31 v32  
    133133{{{
    134134java -jar /usr/local/share/picard-tools/CollectRnaSeqMetrics.jar INPUT=accepted_hits.bam REF_FLAT=refFlat.txt STRAND_SPECIFICITY=NONE OUTPUT=Out_RnaSeqMetrics.txt REFERENCE_SEQUENCE=hg19.fa CHART_OUTPUT=Out_RnaSeqMetrics.pdf
     135}}}
     136
     137If you get an "SequenceListsDifferException" error from picard (using a BAM file from TopHat, for example), you may first need to reorder the header BAM header with a command like
     138{{{
     139java -jar /usr/local/share/picard-tools/ReorderSam.jar INPUT=accepted_hits.bam OUTPUT=accepted_hits.reordered.bam REFERENCE=/path/to/reference/genome.fa
    135140}}}
    136141