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Hi there,
my question is about denovo assembly using SOAP denovo-trans. I have data from a MiSeq, 20 Mio paired end reads, 250bp each, with some overlap in the middle depending on the library prep.
I filter these reads according to their quality (Q20, 90%) and trim the end of the reads for the left side sequences, because they tend to be lower quality. This means afterwards some sequences become single reads, the second read being discarded.
SOAP supports the use of paired end reads, and my input would then be two files (right and left sequence). I coudn't find info on how it treats "missing" reads, does anybody knows whether it slows down the process, or it doesn't matter?
Also, is it useful to merge the reads before doing the assembly? Since during the library prep the fragment size was around 500 bp and I have 2x 250bp...
Thanks for your help!
Mathilde
my question is about denovo assembly using SOAP denovo-trans. I have data from a MiSeq, 20 Mio paired end reads, 250bp each, with some overlap in the middle depending on the library prep.
I filter these reads according to their quality (Q20, 90%) and trim the end of the reads for the left side sequences, because they tend to be lower quality. This means afterwards some sequences become single reads, the second read being discarded.
SOAP supports the use of paired end reads, and my input would then be two files (right and left sequence). I coudn't find info on how it treats "missing" reads, does anybody knows whether it slows down the process, or it doesn't matter?
Also, is it useful to merge the reads before doing the assembly? Since during the library prep the fragment size was around 500 bp and I have 2x 250bp...
Thanks for your help!
Mathilde