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-   -   bowtie- paired end - no alignments (http://seqanswers.com/forums/showthread.php?t=12244)

madsaan 06-22-2011 02:52 PM

bowtie- paired end - no alignments
 
Hi my command for a paired end read is as follows:

./bowtie -v 0 -a -p 2 -X 300 hg19 -c -1 TGGGAGATATACCTAATGCTAGATGACCCA, -2 AAGTTTAGGGTACATGTGCAGGTTAGTTA


and am getting a message that says

reads that failed to align - 1(100%)

am not sure if am going wrong with the syntax.it works when I do them as single-end reads.

help!!
thanks

madsaan 06-27-2011 01:24 PM

OK.figured it out!!


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