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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
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