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Old 06-22-2011, 02:52 PM   #1
madsaan
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Location: california

Join Date: Jan 2011
Posts: 26
Default 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

Last edited by madsaan; 06-27-2011 at 03:56 PM.
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