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  • adamdeluca
    replied
    looks like you need the beta version for the makePairedFile task
    http://www.broadinstitute.org/softwa...re/?q=download

    Leave a comment:


  • memo
    started a topic scripture trouble

    scripture trouble

    Hi!

    I'm trying to use scripture to assemble RNAseq reads, and when preprocessing the data I use this command:

    java -Xmx4000m -jar scripture.jar -task makePairedFile -pair1 spm31/good_hits.sorted.sam -pair2 spm32/good_hits.sorted.sam -out lane3.paired.sam -sorted

    This gives me the message "Invalid task makePairedFile" in return.

    Anyone here who has used scripture and knows what goes wrong?

    Have a nice day!
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