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Question: Unmapped Reads From Tophat
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gravatar for Kevin Y
6.0 years ago by
Kevin Y • 10
Kevin Y • 10 wrote:
Hello, Is there a way to get unmapped reads from tophat? The accepted hits bam output only contains mapped reads (confirmed with flagstat) Am I overlooking an option or tool? Thanks Kevin
rna-seq tophat • 2.1k views
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modified 6.0 years ago by Ido M. Tamir • 280 • written 6.0 years ago by Kevin Y • 10
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gravatar for Ido M. Tamir
6.0 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
Only the very latest tophat version 1.4.1 IIRC (and maybe tophat2 from the beginning) save unmapped reads into a fastq.gz file output, and its not an option. I don't think the galaxy output puts this into your history yet. best, ido
ADD COMMENT • link written 6.0 years ago by Ido M. Tamir • 280
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