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Old 10-13-2009, 01:59 PM   #2
Cole Trapnell
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Location: Boston, MA

Join Date: Nov 2008
Posts: 212
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You appear to have the reads separated by spaces and commas. The left reads should be a single comma separated list, and same for the right. Like this:

tophat --solexa1.3-quals -m 1 -r 130 -G /datastore/nextgenproc/projects/exonDB/custom_exonDB.04152009.hg18.exon.gff /home/jyli/Bowtie/indexes/hg18_genome
../raw_data/MCF7_CP7_00300_003_s_4_1.txt,../raw_data/MCF7_CP7_00300_008_s_7_1.txt ../raw_data/MCF7_CP7_00300_003_s_4_2.txt,../raw_data/MCF7_CP7_00300_008_s_7_2.txt
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