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Old 07-19-2012, 08:08 AM   #1
NRiddiford
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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 (http://github.com/audy/stitch),
SHERA (http://almlab.mit.edu/vibrioGenomes/SHERA_temp/),
SeqPrep (http://seqanswers.com/wiki/SeqPrep) and
FLASH (http://genomics.jhu.edu/software/FLASH/index.shtml)

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,

Nick
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