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ChrisMaherLab / INTEGRATE

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Merged BAM from TopHat2 #2

Closed jasonwalker80 closed 8 years ago

jasonwalker80 commented 8 years ago

@jin-wash-u

Is there a way to provide a combined, merged BAM file with both mapped and unmapped reads from TopHat2? Or do I need to split the mapped and unmapped before running Integrate?

jin-wash-u commented 8 years ago

INTEGRATE can handle both merged file and split files:

Integrate fusion reference.fasta annot.txt ./bwts merged.bam merged.bam dna.tumor.bam dna.normal.bam

or

Integrate fusion reference.fasta annot.txt ./bwts accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam

where merged.bam is merged from accepted_hits.bam unmapped.bam.