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Old 06-06-2011, 01:30 PM   #1
clariet
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Location: NJ

Join Date: Mar 2010
Posts: 18
Default problem running runRNA.pl in CASAVA for RNA-seq data with multiple indexes

I have a RNA-seq dataset run in one lane from Illumina. Each sample has 3 indexes.

I have ran demultiplex.pl and Gerald.pl successful. Now I have export file in each individual index folder. I need to run runRNA.pl to get RNA counts. But I couldn't combine multiple export directory. My command line is like this:

/CASAVA-1.7.0-build/bin/runRNA.pl --projectDir=CASAVA.RNA.build_s1 \
--targets configure --runId=110503_HWUSI-EAS1800_00019_FC \ --exportDir=001/GERALD_25-05-2011_haol -l 7 \
--runId=110503_HWUSI-EAS1800_00019_FC \ --exportDir=002/GERALD_26-05-2011_haol -l 7 \
--runId=110503_HWUSI-EAS1800_00019_FC \ --exportDir=004/GERALD_27-05-2011_haol -l 7 \
--refFlatFile=/Home/haol/GENOMES/Human/Homo_sapiens/UCSC/hg19/Annotation/Genes/refFlat.txt.gz \
--refSequences /Home/haol/GENOMES/Human/Homo_sapiens/UCSC/hg19/Sequence/Squashed-Homo_sapiens-UCSC-hg19

but no task file generated. Any input? I really appreciate it!
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