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Old 02-15-2011, 01:02 AM   #3
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Location: China

Join Date: Feb 2009
Posts: 116

Originally Posted by dariober View Post
Hi pengchy,

Try to upgrade to the latest versions of Bowtie and Tophat. In particular Bowtie <0.12.7 seem to have issues with all-gap sequence (see

Having said this, I'm also finding the warning "Warning: Encountered reference sequence with only gaps" and I'm using the latest versions. Curiously, I get the warnings when I align 57 bp reads but no warnings with 35 bp reads.
Yes, as you say, the warning still output when we upgrade the bowtie to version 0.12.7.
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