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Old 11-08-2012, 10:39 PM   #7
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66

First of all thank you for your help. I would like to add all the possible support to your rant, I'm worried that this is shoddy science also

I looked at those reads qualities with fastqc and for some samples they are terrible, but for the one that I showed here I don't notice a tremendous fall of qualities at the end of reads.

Originally Posted by dvanic View Post

Coming back to your problem (and I know this is not exactly a solution) - have you tried using 2.0.5/6 on your reads? I've had much better results (am more happy with how the mapping "looks") with the .5 version, since it does seem to improve mapping accuracy by using both genome and transcriptome as a reference. Perhaps there was a bug in 2.0.0 that has been fixed in the later versions?...
The reports did not cite something similar but I'm definitely willing to try. I'm worried because in the past I used tophat 2.0.0 and I did not notice any number of reads inconsistency but bug bites bug...
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