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Old 07-19-2012, 08:08 AM   #1
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Location: Ireland

Join Date: Jul 2012
Posts: 6
Default Overlapping Paired End reads - questions...

Hi guys,

I've just received my first RNA-Seq data back from sequencing.

The company I used did chemical RNA fragmentation, which apparently produces more size-consistent, albeit smaller, fragments and thus, with 100bp PE reads, I have overlap in the majority of reads.

From reading these discussions it seem like I have two options: either merge into long SE reads, or run in top hat with -ve insert length specified. I think I'm going to try both for comparison, but I have a few questions:

Firstly, what is the best tool for assembling overlapping reads? I have seen mention of -

Stitch (,
SeqPrep ( and

What are the recommendations?

Secondly, If I'm to specify the negative insert length in tophat, I need to know the extent which they overlap - do any/all of the these programmes do this?

Many thanks,

NRiddiford is offline   Reply With Quote

overlap, paried end, rna-seq, tophat

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