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7.3 years ago
arnstrm ★ 1.8k

Hi all,

I have few questions about MaSuRCA assembly program and I will greatly appreciate if anyone can clarify these doubts:

1. 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.
2. How to specify the overlapping libraries ? The sr-config file asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, but negative mean are to specify paired-end reads that are outies (RF) and it won't accept 0 as insert size. Also, is the mean, insert-size or the total size (read length * 2 + insert size)?
3. 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,

masurca assembly paired end mate pairs • 4.0k views
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7.3 years ago
rtliu ★ 2.1k

1. No need to run trimmomatic. the inbuilt error correction step has adapter trimming, error correction, etc.

2. Read the quick start guide (ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf).  e.g.

The 'mean' and 'stdev' parameters are the library insert average length and standard deviation.

"JUMP are assumed to be outties <---.--->. If there are any jump libraries that are innies, such as longjump,

specify them as JUMP and specify NEGATIVE mean."  So negative mean is for longjump library, not

3. No, you can specify each library per line, e.g. add a new line, supposed 250bp PE library with 30bp stdev

Good luck!

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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!

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insert size = 450bp