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Old 08-25-2011, 11:21 AM   #1
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Location: La Jolla, CA

Join Date: Aug 2011
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Default Convert SOAPsplice v1.4 output to SAM

Hi all, I'm trying to use SOAPsplice 1.4 to align some paired end reads. The alignment works fine, but the output is a custom format. Does anyone know how to convert the SOAPsplice ouput to SAM or have a script to do this? Thanks!

Note: I realize v1.4 of SOAPsplice "supports" output to SAM, but only from the soapsplice executable. However, the example included with the SOAPsplice download makes use of a few more scripts after the soapsplice executable, making the SAM output useless (not to mention I'm getting an error when I try to generate a SAM file from the soapsplice executable).
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convert, output, rna-seq, sam, soapsplice

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