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Old 10-17-2011, 11:24 AM   #1
plassaaw
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Default Bowtie2 with Tophat

Hi,

Does anyone have any experience using Bowtie2 with Tophat?

If so could you send me your tophat script?
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Old 10-17-2011, 07:26 PM   #2
plassaaw
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Never mind. I figured it out.
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Old 10-18-2011, 05:17 PM   #3
nilshomer
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Quote:
Originally Posted by plassaaw View Post
Never mind. I figured it out.
Please share for those who will see this later.
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Old 10-19-2011, 09:15 AM   #4
plassaaw
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I posted that as i got it running.. It eventually core dumped and I spoke with the designers of tophat and they said it will take serious conversions, since bwt2 uses only sam output files instead of the bwtout as before and the -un command no longer exists and the unaligned reads are in the bam file. I decided I was better off waiting for them to release an update.
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Old 11-11-2011, 06:12 AM   #5
Nicolas
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Did they say they will make an update of Tophat using Bowtie2?
It would be great, so long as the Tophat output can provide accurate Mapping Quality (MAPQ field in SAM format), which Bowtie2 does...
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