Hi all,
I have few questions about MaSuRCA
assembly program and I will greatly appreciate if anyone can clarify these doubts:
- Do I have to run
trimmomatic
or any other filtering/trimming tools before I run the assembly? I am asking this because the program already has a inbuilt error correction step. - How to specify the
overlapping libraries
? Thesr-config
file asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, butnegative mean
are to specifypaired-end
reads that areouties (RF)
and it won't accept0
as insert size. Also, is the mean, insert-size or the total size(read length * 2 + insert size)
? - Do I have to combine similar library types into a single file before putting them in
sr-config
file or is it OK to specify each library separately?
Thanks very much,
Thanks very much for answering! I am still not getting the second question. If I have overlapping libraries (miseq) of length 250bp (R1=250bp, R2=250bp), with 50bp overlap, what would be the insert size? will it be the total length (450bp) or insert size (-50bp)?
Thanks once again!
insert size = 450bp