tophat-recondition
post-processor for TopHat unmapped reads
Description
tophat-recondition is a post-processor for TopHat unmapped reads (contained in unmapped.bam), making them compatible with downstream tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It also works around bugs in TopHat: * the "mate is unmapped" SAM flag is not set on any reads in the
unmapped.bam file (TopHat issue #3)
* the mapped mate of an unmapped read can be absent from
accepted_hits.bam, creating a mismatch between the file and the unmapped
read's flags (TopHat issue #16)
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Homepage
https://github.com/cbrueffer/tophat-recondition
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