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Old 01-25-2018, 08:39 AM   #1
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Default Merging PE reads before de novo RNA-Seq assembly

can someone please give an opinion: does that make sense to merge PE reads before a de novo RNA-seq assembly (say with Trinity)?
Merging tools are quite fast (like USEARCH, and the amount of raw data is reduced drastically. Can merged data be suitable for further assembly in a “single-ends” mode, or am I missing some theory behind it?.. Seems like it may save a lot of computations.

Thanks in advance.
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Old 01-25-2018, 09:38 AM   #2
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For reference cross-posted to:
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Old 01-26-2018, 04:11 AM   #3
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I've never understood why people think that pair-merging prior to de novo assembly is a good idea. Seems like were that the case, assembly engines would just do pair-merging themselves prior to other assembly steps.

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assembly, pe reads, rna-seq, trinity, usearch

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