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Old 12-20-2010, 12:52 AM   #1
Location: Jerusalem

Join Date: May 2010
Posts: 26
Default Gapped alignment with RNA-Seq

It seems that the mainstream tools used for RNA-Seq analysis are Tophat and Cufflinks. However, since Tophat is bowtie-based it can't do gapped alignment with short reads. I thought of mapping with BWA and using the resulting SAM with Cufflinks, but as BWA is not meant for RNA-Seq alignment I am hesitant. Does anyone know of an RNA-Seq aligner that supports gapped alignment?
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Old 12-20-2010, 06:45 AM   #2
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Location: Stuttgart, Germany

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it shows off some really nice result. Hope that helps.

regards sphil
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Old 12-21-2010, 08:03 PM   #3
Location: Melbourne

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I couldn't seem to find anything suggesting QPALMA solves the problem of gapped alignment. Specifically I couldn't find anything about gapped alignments in vmatch which QPALMA uses.

Am I not mistaken?
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