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Old 04-22-2010, 04:34 AM   #1
damiankao
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Location: UK

Join Date: Jan 2010
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Default bowtie and cufflinks

I have several .csfasta and corresponding .qual files from ABI runs. The readIDs from the multiple csfasta files could be the same. I want to concatenate all of them into a single file. Does Bowtie care if my .csfasta file have entries with same header name?

And will Cufflinks care about duplicate read IDs in the resulting .sam file?
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