Sorry if this is in the wrong place. There are quite a few spots this could have gone. I've done some poking around, and haven't quite found an answer to my question, which is:
I am attempting to assemble a denovo transcript using paired end illumina 3000 reads from 4 different treatments, with 3 biological reps per treatment.
To do an assembly de novo, is it kosher (or better yet, is it required) to join all the reps from all the treatments into one "super-reads" file for R1 and another for the R2? If so, do I have to cat them in the same order to allow the correct R1 read to pair with its correct R2 read? Is there anyway to avoid this, and just give trinity all of the read files individually?
I am attempting to assemble a denovo transcript using paired end illumina 3000 reads from 4 different treatments, with 3 biological reps per treatment.
To do an assembly de novo, is it kosher (or better yet, is it required) to join all the reps from all the treatments into one "super-reads" file for R1 and another for the R2? If so, do I have to cat them in the same order to allow the correct R1 read to pair with its correct R2 read? Is there anyway to avoid this, and just give trinity all of the read files individually?
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