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Old 01-12-2012, 03:56 PM   #4
RogerH
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Location: Townsville, Australia

Join Date: Dec 2011
Posts: 6
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Hi,

Thanks for the reply. Yes, I'm using Illumina 100bp paired-end data.

My supervisor told me that I should just try trimmed and untrimmend, and then suggested that I use the untrimmed assembly for annotation. But I did fear that there might be a problem with that.

I used FastQC on my data, there is a bit of a problem with the GCAT content in the first 10 bp (due to the not-so-random random primers that are used for Illumina library preparation I believe). And the Q value of the last 15-20 bases drops off considerably.

The problem is that I'm pressed for time, so before Christmas I decided to stop working on the assembly and go ahead with the annotation step (which takes a considerable amount of time, using Blast2go).
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