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Old 04-02-2014, 12:44 AM   #3
areyes
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Location: Heidelberg

Join Date: Aug 2010
Posts: 165
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Hi kajot,

I have the feeling that could be related to the protocol that you are using. In the most recent protocol of the illumina runs (at least the latest used by the sequencing facility at EMBL), you get strand specific data, but the reads map opposite to the strand where they come from. For example, for a gene that is in the forward strand, you will get all the reads mapping to the reverse strand. This is a it confusing!

So, what I recommend is that in your IGV browser you could colour your reads depending on the strand where they map to, and then see if what I describe above is the case. If so, I think the parameter "-s reverse" parameter of the dexseq_count.py script should do the trick.

Alejandro
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