bowtie and cufflinks

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damiankao

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Join Date: Jan 2010

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#1

bowtie and cufflinks

04-22-2010, 03:34 AM

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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