Hi all,
We've recently completed a run of 454 sequences from the transcriptome of a reef-building coral, and I am in the process of attempting de novo assembly. Since it seems Euler-SR does better on this type of data than Newbler or CAP3, I am trying this software. But Im finding the output kind of hard to interpret.
Does anyone know of a good set of instructions for using this software? Anything specifically geared toward transcriptome, rather than genome, assembly would be especially useful.
On a more detailed note, does anyone know the following regarding the output of Euler-SR?
1. Is it possible to view singletons, and if so, where is that file?
2. Is there any output that describes the mapping of reads to contigs? (as, for example, was easily parsed from CAP3 output).
3. On what basis are reads excluded prior to assembly (e.g., for my test set of 2500 reads only 2477 were included at the beginning of assembly). And how can this behavior be adjusted if needed?
Thank for your any advice you might have,
-Eli
We've recently completed a run of 454 sequences from the transcriptome of a reef-building coral, and I am in the process of attempting de novo assembly. Since it seems Euler-SR does better on this type of data than Newbler or CAP3, I am trying this software. But Im finding the output kind of hard to interpret.
Does anyone know of a good set of instructions for using this software? Anything specifically geared toward transcriptome, rather than genome, assembly would be especially useful.
On a more detailed note, does anyone know the following regarding the output of Euler-SR?
1. Is it possible to view singletons, and if so, where is that file?
2. Is there any output that describes the mapping of reads to contigs? (as, for example, was easily parsed from CAP3 output).
3. On what basis are reads excluded prior to assembly (e.g., for my test set of 2500 reads only 2477 were included at the beginning of assembly). And how can this behavior be adjusted if needed?
Thank for your any advice you might have,
-Eli
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