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Old 01-13-2012, 07:19 AM   #1
Location: Birmingham, Al

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Default CSHL Long RNA-seq dataset

I have uploaded the CSHL Long RNA-seq fastq dataset from the UCSC genome browser to galaxy and attempted to map the reads using bowtie, bwa and tophat. None of them are able to align more than a super small fraction of the reads. I have used each of these programs to align exactly the same types fastq data before, and it has worked perfectly. Does anyone have any suggestions as to what the problem could be?
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Old 01-13-2013, 11:20 PM   #2
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the raw data could be a combination of left part and right part of each fragment. You should try SRA toolkit first to split it into two lifes and then mapping.
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