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Forum: Illumina/Solexa 03-13-2015, 10:51 AM
Replies: 58
Views: 52,728
Posted By fanli
Yep. Tbh, I'm not sure what happens if you...

Yep. Tbh, I'm not sure what happens if you reverse the r1 and r2 files - I suppose most of the pairs get thrown away for being discordantly paired but have never tried.
Forum: Illumina/Solexa 03-13-2015, 10:13 AM
Replies: 58
Views: 52,728
Posted By fanli
You want tophat --library-type fr-firststrand...

You want
tophat --library-type fr-firststrand seq_1.txt seq_2.txt

Of course, I'd check that your libraries are indeed in the correct orientation by doing what dvanic did. I recently found out...
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