Merging PE reads before de novo RNA-Seq assembly

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6.2 years ago

roussine ▴ 10

Hello! 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 www.drive5.com/usearch/manual/merge_pair.html) 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. Leo

RNA-Seq PE reads Assembly USEARCH • 1.5k views

ADD COMMENT • link 6.2 years ago by roussine ▴ 10

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Do you have a dataset that is largely merging? That indicates that insert sizes are much smaller that normally is the case. You could use that part of the data (which is able to merge) as single-end reads which will have sampled the entire fragment.

ADD REPLY • link 6.2 years ago by GenoMax 141k

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Yes, it quite merges, a good peak at about 170 bases (~ 4/5 of all 100 bases-reads merge). Do I get right that you do not see any contras against using the merged portion for SE assemblies?

ADD REPLY • link 6.2 years ago by roussine ▴ 10

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